printf '

' | fink --no-use-binary-dist --yes  --build-as-nobody rebuild r-base215 2>&1
WARNING: your info file index has not been updated for 22 days. You should
run 'fink selfupdate' to get the latest package descriptions.
The package 'r-base215' will be built without being installed.
Reading build dependency for r-base215-2.15.3-112...
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The package 'bzip2-dev' will be installed.
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The package 'cairo' will be installed.
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The package 'fontconfig2-dev' will be installed.
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The package 'freetype219' will be installed.
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The package 'glib2-dev' will be installed.
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The package 'gcc49-compiler' will be installed.
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The package 'libgettext8-dev' will be installed.
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The package 'libiconv-dev' will be installed.
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The package 'libicu48-dev' will be installed.
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The package 'flag-sort' will be installed.
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The package 'freetype219-shlibs' will be installed.
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The package 'libmpfr4-shlibs' will be installed.
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The package 'cloog-org2-shlibs' will be installed.
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The package 'isl-shlibs' will be installed.
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The package 'libmpc3-shlibs' will be installed.
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The package 'gettext-bin' will be installed.
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The package 'libjpeg-bin' will be installed.
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The package 'pango1-xft2-ft219' will be installed.
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The package 'tcltk-shlibs' will be installed.
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The package 'pixman-shlibs' will be installed.
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The package 'xdg-base' will be installed.
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The package 'libjbig-shlibs' will be installed.
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The package 'libthai-shlibs' will be installed.
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The package 'xft2-shlibs' will be installed.
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The package 'fontconfig-config' will be installed.
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The package 'libdatrie1-shlibs' will be installed.
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The package 'libthai' will be installed.
Reading dependency for libthai-0.1.20-1...
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The following package will be rebuilt:
 r-base215
The following 53 additional packages will be installed:
 bzip2-dev cairo cairo-shlibs cloog-org2-shlibs expat1-shlibs
 fink-package-precedence flag-sort fontconfig-config fontconfig2-dev
 fontconfig2-shlibs freetype219 freetype219-shlibs gcc49-compiler
 gcc49-shlibs gettext-bin glib2-dev glib2-shlibs gmp5-shlibs isl-shlibs
 libdatrie1-shlibs libgettext8-dev libgmpxx5-shlibs libiconv-dev libicu48-dev
 libicu48-shlibs libjbig-shlibs libjpeg-bin libjpeg9 libjpeg9-shlibs liblzma5
 liblzma5-shlibs libmpc3-shlibs libmpfr4-shlibs libpcre1 libpcre1-shlibs
 libpng16 libpng16-shlibs libthai libthai-shlibs libtiff5 libtiff5-shlibs
 pango1-xft2-ft219 pango1-xft2-ft219-dev pango1-xft2-ft219-shlibs
 pixman-shlibs pkgconfig readline6 readline6-shlibs tcltk tcltk-dev
 tcltk-shlibs xdg-base xft2-shlibs
Do you want to continue? [Y/n] (assuming default)
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* History: (history). The GNU history library API.
install-info(/sw/share/info/history.info): creating new section `Libraries'
* Readline: (readline). The GNU readline library API.
* RLuserman: (rluserman). The GNU readline library User's Manual.

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R-2.15.3/
R-2.15.3/ChangeLog
R-2.15.3/config.site
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R-2.15.3/INSTALL
R-2.15.3/m4/
R-2.15.3/m4/bigendian.m4
R-2.15.3/m4/cairo.m4
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R-2.15.3/m4/gettext-lib.m4
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R-2.15.3/m4/lt~obsolete.m4
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R-2.15.3/README
R-2.15.3/share/
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R-2.15.3/share/java/README
R-2.15.3/share/licenses/
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R-2.15.3/share/licenses/license.db
R-2.15.3/share/make/
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R-2.15.3/src/
R-2.15.3/src/appl/
R-2.15.3/src/appl/bakslv.c
R-2.15.3/src/appl/binning.c
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R-2.15.3/src/appl/cpoly.c
R-2.15.3/src/appl/cumsum.c
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R-2.15.3/tests/ok-errors.R
R-2.15.3/tests/ok-errors.Rout.save
R-2.15.3/tests/p-r-random-tests.R
R-2.15.3/tests/p-r-random-tests.Rout.save
R-2.15.3/tests/Pkgs/
R-2.15.3/tests/Pkgs/exNSS4/
R-2.15.3/tests/Pkgs/exNSS4/DESCRIPTION
R-2.15.3/tests/Pkgs/exNSS4/man/
R-2.15.3/tests/Pkgs/exNSS4/NAMESPACE
R-2.15.3/tests/Pkgs/exNSS4/R/
R-2.15.3/tests/Pkgs/exNSS4/R/nss4.R
R-2.15.3/tests/Pkgs/pkgA/
R-2.15.3/tests/Pkgs/pkgA/DESCRIPTION
R-2.15.3/tests/Pkgs/pkgA/NAMESPACE
R-2.15.3/tests/Pkgs/pkgA/R/
R-2.15.3/tests/Pkgs/pkgA/R/pkgA.R
R-2.15.3/tests/Pkgs/pkgB/
R-2.15.3/tests/Pkgs/pkgB/DESCRIPTION
R-2.15.3/tests/Pkgs/pkgB/NAMESPACE
R-2.15.3/tests/primitives.R
R-2.15.3/tests/print-tests.R
R-2.15.3/tests/print-tests.Rout.save
R-2.15.3/tests/R-intro.Rout.save
R-2.15.3/tests/README
R-2.15.3/tests/reg-BLAS.R
R-2.15.3/tests/reg-examples1.R
R-2.15.3/tests/reg-examples2.R
R-2.15.3/tests/reg-IO.R
R-2.15.3/tests/reg-IO.Rout.save
R-2.15.3/tests/reg-IO2.R
R-2.15.3/tests/reg-IO2.Rout.save
R-2.15.3/tests/reg-packages.R
R-2.15.3/tests/reg-plot-latin1.pdf.save
R-2.15.3/tests/reg-plot-latin1.R
R-2.15.3/tests/reg-plot.pdf.save
R-2.15.3/tests/reg-plot.R
R-2.15.3/tests/reg-plot.Rout.save
R-2.15.3/tests/reg-S4.R
R-2.15.3/tests/reg-S4.Rout.save
R-2.15.3/tests/reg-tests-1a.R
R-2.15.3/tests/reg-tests-1b.R
R-2.15.3/tests/reg-tests-2.R
R-2.15.3/tests/reg-tests-2.Rout.save
R-2.15.3/tests/reg-tests-3.R
R-2.15.3/tests/reg-tests-3.Rout.save
R-2.15.3/tests/reg-win.R
R-2.15.3/tests/simple-true.R
R-2.15.3/tests/simple-true.Rout.save
R-2.15.3/tests/test-system.R
R-2.15.3/tests/test-system.Rout.save
R-2.15.3/tests/test-system2.c
R-2.15.3/tests/testit-Ex.R.save
R-2.15.3/tests/testit.html.save
R-2.15.3/tests/testit.Rd
R-2.15.3/tests/testit.tex.save
R-2.15.3/tests/testit.txt.save
R-2.15.3/tests/utf8-regex.R
R-2.15.3/tests/ver20-Ex.R.save
R-2.15.3/tests/ver20.html.save
R-2.15.3/tests/ver20.Rd
R-2.15.3/tests/ver20.tex.save
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R-2.15.3/tests/WinUnicode.dat
R-2.15.3/tools/
R-2.15.3/tools/config.guess
R-2.15.3/tools/config.rpath
R-2.15.3/tools/config.sub
R-2.15.3/tools/copy-if-change
R-2.15.3/tools/GETCONFIG
R-2.15.3/tools/GETDISTNAME
R-2.15.3/tools/GETMAKEVAL
R-2.15.3/tools/getsp.class
R-2.15.3/tools/getsp.java
R-2.15.3/tools/GETVERSION
R-2.15.3/tools/help2man.pl
R-2.15.3/tools/install-info.pl
R-2.15.3/tools/install-sh
R-2.15.3/tools/ldAIX4
R-2.15.3/tools/link-recommended
R-2.15.3/tools/ltmain.sh
R-2.15.3/tools/Makefile.in
R-2.15.3/tools/mdate-sh
R-2.15.3/tools/missing
R-2.15.3/tools/move-if-change
R-2.15.3/tools/README
R-2.15.3/tools/rsync-recommended
R-2.15.3/tools/updatefat
R-2.15.3/VERSION
R-2.15.3/VERSION-NICK
sudo -u fink-bld [ENV] sh -c /tmp/fink.pb8S1
[ -r /sw/fink/dists/stable/main/finkinfo/sci/r-base215.patch ]
sudo -u fink-bld [ENV] sh -c /tmp/fink.NJzn0
patch -p1 < /sw/fink/dists/stable/main/finkinfo/sci/r-base215.patch
patching file Makeconf.in
Hunk #1 succeeded at 78 (offset -5 lines).
patching file Makefile.fw
patching file configure
patching file src/main/Makefile.in
patching file src/nmath/standalone/Makefile.in
perl -pi -e 's/-undefined dynamic_lookup//' configure
sudo -u fink-bld [ENV] sh -c /tmp/fink.utBkn
/tmp/fink.EqEwu
#!/bin/sh -efv
  
  export F77=/sw/bin/gfortran-fsf-4.9
  export FC=/sw/bin/gfortran-fsf-4.9
    
  unset R_HOME
  ./configure --prefix=/sw   --libdir='/sw/lib' --mandir='${prefix}/share/man' \
  --with-blas="-framework Accelerate" \
  --with-lapack="-framework Accelerate" \
  --with-aqua --enable-R-framework=/sw/Library/Frameworks \
  --with-system-bzlib --with-system-pcre --with-system-zlib \
  --with-x --x-includes=/usr/X11R6/include --x-libraries=/usr/X11R6/lib \
  --with-tcl-config=/sw/lib/tclConfig.sh --with-tk-config=/sw/lib/tkConfig.sh CFLAGS="-g -O3" CXXFLAGS="-g -O3" FFLAGS="-g -O3" SED="/usr/bin/sed"
checking build system type... x86_64-apple-darwin13.3.0
checking host system type... x86_64-apple-darwin13.3.0
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
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checking for gawk... no
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checking whether ln -s works... yes
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checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
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checking for which... /sw/bin/which
checking for less... /usr/bin/less
checking for gtar... /sw/bin/gtar
checking for tex... no
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configure: WARNING: you cannot build PDF versions of the R manuals
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configure: WARNING: you cannot build PDF versions of vignettes and help pages
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checking whether makeinfo version is at least 4.7... yes
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using default browser ... /usr/bin/open
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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 flag-sort -r gcc -ffor-scope accepts -g... yes
checking for flag-sort -r gcc -ffor-scope option to accept ISO C89... none needed
checking how to run the C preprocessor... flag-sort -r gcc -ffor-scope -E
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checking for egrep... /usr/bin/grep -E
checking whether flag-sort -r gcc -ffor-scope needs -traditional... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
no
checking how to run the C preprocessor... flag-sort -r gcc -ffor-scope -E
defining F77 to be /sw/bin/gfortran-fsf-4.9
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether /sw/bin/gfortran-fsf-4.9 accepts -g... yes
checking whether we are using the GNU C++ compiler... yes
checking whether flag-sort -r g++ accepts -g... yes
checking how to run the C++ preprocessor... flag-sort -r g++ -E
checking whether __attribute__((visibility())) is supported... no
checking whether flag-sort -r gcc -ffor-scope accepts -fvisibility... yes
checking whether /sw/bin/gfortran-fsf-4.9 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 for gcc... gcc
checking whether we are using the GNU Objective C compiler... yes
checking whether gcc accepts -g... yes
checking for Objective C++ compiler... trying some possibilities
checking whether flag-sort -r g++ can compile ObjC++... yes
flag-sort -r g++
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 flag-sort -r gcc -ffor-scope... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/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 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/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 flag-sort -r gcc -ffor-scope 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 flag-sort -r g++ accepts -g... (cached) yes
checking how to run the C++ preprocessor... flag-sort -r g++ -E
checking whether we are using the GNU Fortran 77 compiler... (cached) yes
checking whether /sw/bin/gfortran-fsf-4.9 accepts -g... (cached) yes
checking for objdir... .libs
checking if flag-sort -r gcc -ffor-scope supports -fno-rtti -fno-exceptions... yes
checking for flag-sort -r gcc -ffor-scope option to produce PIC... -fno-common -DPIC
checking if flag-sort -r gcc -ffor-scope PIC flag -fno-common -DPIC works... yes
checking if flag-sort -r gcc -ffor-scope static flag -static works... no
checking if flag-sort -r gcc -ffor-scope supports -c -o file.o... yes
checking if flag-sort -r gcc -ffor-scope supports -c -o file.o... (cached) yes
checking whether the flag-sort -r gcc -ffor-scope linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin13.3.0 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 flag-sort -r g++... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no
checking whether the flag-sort -r g++ linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking for flag-sort -r g++ option to produce PIC... -fno-common -DPIC
checking if flag-sort -r g++ PIC flag -fno-common -DPIC works... yes
checking if flag-sort -r g++ static flag -static works... no
checking if flag-sort -r g++ supports -c -o file.o... yes
checking if flag-sort -r g++ supports -c -o file.o... (cached) yes
checking whether the flag-sort -r g++ linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin13.3.0 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 /sw/bin/gfortran-fsf-4.9 option to produce PIC... -fno-common
checking if /sw/bin/gfortran-fsf-4.9 PIC flag -fno-common works... yes
checking if /sw/bin/gfortran-fsf-4.9 static flag -static works... no
checking if /sw/bin/gfortran-fsf-4.9 supports -c -o file.o... yes
checking if /sw/bin/gfortran-fsf-4.9 supports -c -o file.o... (cached) yes
checking whether the /sw/bin/gfortran-fsf-4.9 linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin13.3.0 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
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checking for dlfcn.h... (cached) yes
checking elf.h usability... no
checking elf.h presence... no
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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
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checking glob.h usability... yes
checking glob.h presence... yes
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checking grp.h presence... yes
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checking netdb.h usability... yes
checking netdb.h presence... yes
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checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
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checking pwd.h usability... yes
checking pwd.h presence... yes
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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 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 flag-sort -r gcc -ffor-scope option to accept ISO C99... none needed
checking for flag-sort -r gcc -ffor-scope option to accept ISO Standard C... (cached) none needed
checking for inline... inline
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of double... 8
checking size of long double... 16
checking size of size_t... 8
checking whether we can compute C Make dependencies... yes, using flag-sort -r gcc -ffor-scope -MM
checking whether flag-sort -r gcc -ffor-scope supports -c -o FILE.lo... yes
checking for flag-sort -r gcc -ffor-scope option to support OpenMP... unsupported
checking how to get verbose linking output from /sw/bin/gfortran-fsf-4.9... -v
checking for Fortran 77 libraries of /sw/bin/gfortran-fsf-4.9...  -L/sw/lib -L/sw/lib/gcc4.9/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1 -L/sw/lib/gcc4.9/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1/../../.. -lgfortran -lquadmath -lm
checking how to get verbose linking output from flag-sort -r gcc -ffor-scope... -v
checking for C libraries of flag-sort -r gcc -ffor-scope...  -L/sw/lib -lSystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/lib/darwin/libclang_rt.osx.a
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking whether /sw/bin/gfortran-fsf-4.9 appends underscores to external names... yes
checking whether /sw/bin/gfortran-fsf-4.9 appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether /sw/bin/gfortran-fsf-4.9 and flag-sort -r gcc -ffor-scope agree on int and double... yes
checking whether /sw/bin/gfortran-fsf-4.9 and flag-sort -r gcc -ffor-scope agree on double complex... yes
checking for /sw/bin/gfortran-fsf-4.9 option to support OpenMP... -fopenmp
checking whether flag-sort -r g++ accepts -M for generating dependencies... yes
checking for flag-sort -r g++ option to support OpenMP... unsupported
checking whether we can compute ObjC Make dependencies... yes, using gcc -MM
checking for ObjC runtime library... -lobjc
checking for ObjC runtime style... next
checking whether gcc 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 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 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 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 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 utime exists and is declared... yes
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 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 for cblas_cdotu_sub in vecLib framework... -framework vecLib
checking for dgemm_ in -framework Accelerate... yes
checking whether double complex BLAS can be used... yes
checking whether the BLAS is complete... yes
checking for dpstrf_... yes
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... yes
checking for X... libraries /usr/X11R6/lib, headers /usr/X11R6/include
checking whether -R must be followed by a space... neither works
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking X11/Intrinsic.h usability... yes
checking X11/Intrinsic.h presence... no
configure: WARNING: X11/Intrinsic.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: X11/Intrinsic.h: proceeding with the compiler's result
checking for X11/Intrinsic.h... yes
checking for XtToolkitInitialize in -lXt... yes
using X11 ... yes
checking for KeySym... yes
checking X11/Xmu/Atoms.h usability... yes
checking X11/Xmu/Atoms.h presence... no
configure: WARNING: X11/Xmu/Atoms.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: X11/Xmu/Atoms.h: proceeding with the compiler's result
checking for X11/Xmu/Atoms.h... yes
checking for XmuInternAtom in -lXmu... yes
checking whether pkg-config knows about cairo and pango... yes
checking whether cairo including pango is >= 1.2 and works... yes
checking for CFStringGetSystemEncoding in CoreFoundation framework... -framework CoreFoundation
checking for /sw/lib/tclConfig.sh... /sw/lib/tclConfig.sh
checking for /sw/lib/tkConfig.sh... /sw/lib/tkConfig.sh
checking tcl.h usability... yes
checking tcl.h presence... yes
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checking tk.h usability... yes
checking tk.h presence... yes
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checking whether compiling/linking Tcl/Tk code works... yes
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checking if jpeglib version >= 6b... yes
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checking for main in -lz... yes
checking if libpng version >= 1.2.7... yes
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checking tiffio.h usability... yes
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checking rpc/types.h usability... yes
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checking zlib.h usability... yes
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checking whether zlib support needs to be compiled... no
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checking bzlib.h usability... yes
checking bzlib.h presence... yes
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checking if bzip2 version >= 1.0.6... yes
checking whether bzip2 support needs to be compiled... no
checking for lzma_version_number in -llzma... yes
checking lzma.h usability... yes
checking lzma.h presence... yes
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checking if lzma version >= 4.999... yes
checking for pcre_fullinfo in -lpcre... yes
checking pcre.h usability... yes
checking pcre.h presence... yes
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checking pcre/pcre.h usability... no
checking pcre/pcre.h presence... no
checking for pcre/pcre.h... no
checking if PCRE version >= 7.6... yes
checking whether PCRE support needs to be compiled... no
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
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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 for java... /usr/bin/java
checking for javac... /usr/bin/javac
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checking for jar... /usr/bin/jar
checking whether Java compiler works... yes
checking whether Java interpreter works... yes
checking Java environment... /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
checking for cached Java settings... no
checking whether JNI programs can be compiled... yes
checking whether we are using the GNU Fortran compiler... yes
checking whether /sw/bin/gfortran-fsf-4.9 accepts -g... yes
checking whether we are using the GNU Fortran compiler... (cached) yes
checking whether /sw/bin/gfortran-fsf-4.9 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 /sw/bin/gfortran-fsf-4.9 option to produce PIC... -fno-common
checking if /sw/bin/gfortran-fsf-4.9 PIC flag -fno-common works... yes
checking if /sw/bin/gfortran-fsf-4.9 static flag -static works... no
checking if /sw/bin/gfortran-fsf-4.9 supports -c -o file.o... yes
checking if /sw/bin/gfortran-fsf-4.9 supports -c -o file.o... (cached) yes
checking whether the /sw/bin/gfortran-fsf-4.9 linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin13.3.0 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 /sw/bin/gfortran-fsf-4.9 option to support OpenMP... -fopenmp
checking for recommended packages... yes
checking whether NLS is requested... yes

Configuring src/extra/intl directory
checking whether make sets $(MAKE)... yes
checking for a thread-safe mkdir -p... tools/install-sh -c -d
checking for msgfmt... no
checking for gmsgfmt... :
checking for xgettext... no
checking for msgmerge... no
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... no
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... yes
checking whether to use NLS... yes
checking where the gettext function comes from... external libintl
checking how to link with libintl... -lintl -Wl,-framework -Wl,CoreFoundation
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
config.status: creating etc/Makeconf
config.status: creating etc/Renviron
config.status: creating etc/ldpaths
config.status: creating m4/Makefile
config.status: creating po/Makefile.in
config.status: creating share/Makefile
config.status: creating src/Makefile
config.status: creating src/appl/Makefile
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config.status: creating src/extra/blas/Makefile
config.status: creating src/extra/bzip2/Makefile
config.status: creating src/extra/intl/Makefile
config.status: creating src/extra/pcre/Makefile
config.status: creating src/extra/tre/Makefile
config.status: creating src/extra/xdr/Makefile
config.status: creating src/extra/xz/Makefile
config.status: creating src/extra/zlib/Makefile
config.status: creating src/include/Makefile
config.status: creating src/include/Rmath.h0
config.status: creating src/include/R_ext/Makefile
config.status: creating src/library/Recommended/Makefile
config.status: creating src/library/Makefile
config.status: creating src/library/base/DESCRIPTION
config.status: creating src/library/base/Makefile
config.status: creating src/library/compiler/DESCRIPTION
config.status: creating src/library/compiler/Makefile
config.status: creating src/library/datasets/DESCRIPTION
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config.status: creating src/library/graphics/DESCRIPTION
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config.status: creating src/scripts/R.sh
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config.status: executing libtool commands
config.status: executing po-directories commands
config.status: creating po/POTFILES
config.status: creating po/Makefile
config.status: executing stamp-h commands

R is now configured for x86_64-apple-darwin13.3.0

  Source directory:          .
  Installation directory:    /sw/Library/Frameworks

  C compiler:                flag-sort -r gcc -ffor-scope  -g -O3
  Fortran 77 compiler:       /sw/bin/gfortran-fsf-4.9  -g -O3

  C++ compiler:              flag-sort -r g++  -g -O3
  Fortran 90/95 compiler:    /sw/bin/gfortran-fsf-4.9 -g -O2
  Obj-C compiler:	     gcc -g -O2 -fobjc-exceptions

  Interfaces supported:      X11, aqua, tcltk
  External libraries:        readline, BLAS(generic), LAPACK(generic), ICU, lzma
  Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo
  Options enabled:           framework, R profiling, Java

  Recommended packages:      yes

configure: WARNING: you cannot build PDF versions of the R manuals
configure: WARNING: you cannot build PDF versions of vignettes and help pages
  make
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
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
flag-sort -r gcc -ffor-scope -I. -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c regcomp.c -o regcomp.o
flag-sort -r gcc -ffor-scope -I. -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c regerror.c -o regerror.o
flag-sort -r gcc -ffor-scope -I. -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c regexec.c -o regexec.o
flag-sort -r gcc -ffor-scope -I. -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c tre-ast.c -o tre-ast.o
flag-sort -r gcc -ffor-scope -I. -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c tre-compile.c -o tre-compile.o
flag-sort -r gcc -ffor-scope -I. -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c tre-match-approx.c -o tre-match-approx.o
flag-sort -r gcc -ffor-scope -I. -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c tre-match-backtrack.c -o tre-match-backtrack.o
flag-sort -r gcc -ffor-scope -I. -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c tre-match-parallel.c -o tre-match-parallel.o
flag-sort -r gcc -ffor-scope -I. -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c tre-mem.c -o tre-mem.o
flag-sort -r gcc -ffor-scope -I. -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c tre-parse.c -o tre-parse.o
flag-sort -r gcc -ffor-scope -I. -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c tre-stack.c -o tre-stack.o
flag-sort -r gcc -ffor-scope -I. -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -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 binning.d from binning.c
making bakslv.d from bakslv.c
making cpoly.d from cpoly.c
making cumsum.d from cumsum.c
making fft.d from fft.c
making fmin.d from fmin.c
making integrate.d from integrate.c
making interv.d from interv.c
making lbfgsb.d from lbfgsb.c
making machar.d from machar.c
making maxcol.d from maxcol.c
making pretty.d from pretty.c
making rcont.d from rcont.c
making rowsum.d from rowsum.c
making stem.d from stem.c
making strsignif.d from strsignif.c
making tabulate.d from tabulate.c
making uncmin.d from uncmin.c
making zeroin.d from zeroin.c
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c bakslv.c -o bakslv.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c binning.c -o binning.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c cpoly.c -o cpoly.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c cumsum.c -o cumsum.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c fft.c -o fft.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c fmin.c -o fmin.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c integrate.c -o integrate.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c interv.c -o interv.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c lbfgsb.c -o lbfgsb.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c machar.c -o machar.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c maxcol.c -o maxcol.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c pretty.c -o pretty.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rcont.c -o rcont.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rowsum.c -o rowsum.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c stem.c -o stem.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c strsignif.c -o strsignif.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c tabulate.c -o tabulate.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c uncmin.c -o uncmin.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c zeroin.c -o zeroin.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c ch2inv.f -o ch2inv.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c chol.f -o chol.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dchdc.f -o dchdc.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dpbfa.f -o dpbfa.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dpbsl.f -o dpbsl.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dpoco.f -o dpoco.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dpodi.f -o dpodi.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dpofa.f -o dpofa.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dposl.f -o dposl.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dqrdc.f -o dqrdc.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dqrdc2.f -o dqrdc2.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dqrls.f -o dqrls.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dqrsl.f -o dqrsl.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dqrutl.f -o dqrutl.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dsvdc.f -o dsvdc.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dtrco.f -o dtrco.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dtrsl.f -o dtrsl.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c eigen.f -o eigen.o
rm -f libappl.a
ar cr libappl.a bakslv.o binning.o cpoly.o cumsum.o fft.o fmin.o integrate.o interv.o lbfgsb.o machar.o maxcol.o pretty.o rcont.o rowsum.o stem.o strsignif.o tabulate.o uncmin.o zeroin.o ch2inv.o chol.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 eigen.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 stirlerr.d from stirlerr.c
making gammalims.d from gammalims.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 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 pgamma.d from pgamma.c
making dgamma.d from dgamma.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 plnorm.d from plnorm.c
making dlnorm.d from dlnorm.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 rchisq.d from rchisq.c
making qchisq.d from qchisq.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 dpois.d from dpois.c
making rnbinom.d from rnbinom.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
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c mlutils.c -o mlutils.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c d1mach.c -o d1mach.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c i1mach.c -o i1mach.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c fmax2.c -o fmax2.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c fmin2.c -o fmin2.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c fprec.c -o fprec.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c fround.c -o fround.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c ftrunc.c -o ftrunc.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c sign.c -o sign.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c fsign.c -o fsign.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c imax2.c -o imax2.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c imin2.c -o imin2.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c chebyshev.c -o chebyshev.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c log1p.c -o log1p.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c expm1.c -o expm1.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c lgammacor.c -o lgammacor.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c gammalims.c -o gammalims.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c stirlerr.c -o stirlerr.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c bd0.c -o bd0.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c gamma.c -o gamma.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c lgamma.c -o lgamma.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c gamma_cody.c -o gamma_cody.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c beta.c -o beta.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c lbeta.c -o lbeta.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c polygamma.c -o polygamma.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c bessel_i.c -o bessel_i.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c bessel_j.c -o bessel_j.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c bessel_k.c -o bessel_k.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c bessel_y.c -o bessel_y.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c choose.c -o choose.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c snorm.c -o snorm.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c sexp.c -o sexp.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dgamma.c -o dgamma.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c pgamma.c -o pgamma.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qgamma.c -o qgamma.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rgamma.c -o rgamma.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dbeta.c -o dbeta.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c pbeta.c -o pbeta.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qbeta.c -o qbeta.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rbeta.c -o rbeta.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dunif.c -o dunif.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c punif.c -o punif.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qunif.c -o qunif.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c runif.c -o runif.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dnorm.c -o dnorm.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c pnorm.c -o pnorm.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qnorm.c -o qnorm.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rnorm.c -o rnorm.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dlnorm.c -o dlnorm.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c plnorm.c -o plnorm.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qlnorm.c -o qlnorm.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rlnorm.c -o rlnorm.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c df.c -o df.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c pf.c -o pf.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qf.c -o qf.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rf.c -o rf.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dnf.c -o dnf.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dt.c -o dt.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c pt.c -o pt.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qt.c -o qt.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rt.c -o rt.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dnt.c -o dnt.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dchisq.c -o dchisq.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c pchisq.c -o pchisq.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qchisq.c -o qchisq.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rchisq.c -o rchisq.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rnchisq.c -o rnchisq.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dbinom.c -o dbinom.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c pbinom.c -o pbinom.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qbinom.c -o qbinom.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rbinom.c -o rbinom.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rmultinom.c -o rmultinom.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dcauchy.c -o dcauchy.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c pcauchy.c -o pcauchy.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qcauchy.c -o qcauchy.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rcauchy.c -o rcauchy.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dexp.c -o dexp.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c pexp.c -o pexp.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qexp.c -o qexp.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rexp.c -o rexp.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dgeom.c -o dgeom.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c pgeom.c -o pgeom.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qgeom.c -o qgeom.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rgeom.c -o rgeom.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dhyper.c -o dhyper.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c phyper.c -o phyper.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qhyper.c -o qhyper.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rhyper.c -o rhyper.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dnbinom.c -o dnbinom.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c pnbinom.c -o pnbinom.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qnbinom.c -o qnbinom.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rnbinom.c -o rnbinom.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dpois.c -o dpois.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c ppois.c -o ppois.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qpois.c -o qpois.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rpois.c -o rpois.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dweibull.c -o dweibull.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c pweibull.c -o pweibull.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qweibull.c -o qweibull.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rweibull.c -o rweibull.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dlogis.c -o dlogis.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c plogis.c -o plogis.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qlogis.c -o qlogis.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rlogis.c -o rlogis.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dnchisq.c -o dnchisq.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c pnchisq.c -o pnchisq.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qnchisq.c -o qnchisq.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dnbeta.c -o dnbeta.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c pnbeta.c -o pnbeta.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qnbeta.c -o qnbeta.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c pnf.c -o pnf.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c pnt.c -o pnt.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qnf.c -o qnf.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qnt.c -o qnt.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c ptukey.c -o ptukey.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qtukey.c -o qtukey.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c toms708.c -o toms708.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c wilcox.c -o wilcox.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -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 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 dynload.d from dynload.c
making edit.d from edit.c
making stubs.d from stubs.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
making Rembedded.d from Rembedded.c
making aqua.d from aqua.c
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/usr/X11R6/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dynload.c -o dynload.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/usr/X11R6/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c edit.c -o edit.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/usr/X11R6/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c stubs.c -o stubs.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/usr/X11R6/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c system.c -o system.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/usr/X11R6/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c sys-unix.c -o sys-unix.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/usr/X11R6/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c sys-std.c -o sys-std.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/usr/X11R6/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c X11.c -o X11.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/usr/X11R6/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c Rembedded.c -o Rembedded.o
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/usr/X11R6/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c aqua.c -o aqua.o
rm -rf libunix.a
ar cr libunix.a dynload.o edit.o stubs.o system.o sys-unix.o sys-std.o X11.o Rembedded.o aqua.o
ranlib libunix.a
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/usr/X11R6/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -DR_HOME='"/sw/build.build/r-base215-2.15.3-112/R-2.15.3"' -o Rscript \
	  ./Rscript.c
config.status: creating src/main/Makefile
making CConverters.d from CConverters.c
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 base.d from base.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 cov.d from cov.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 deriv.d from deriv.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 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 fourier.d from fourier.c
making gevents.d from gevents.c
making gram.d from gram.c
making gram-ex.d from gram-ex.c
making gramLatex.d from gramLatex.c
making gramRd.d from gramRd.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 model.d from model.c
making names.d from names.c
making objects.d from objects.c
making optim.d from optim.c
making optimize.d from optimize.c
making options.d from options.c
making par.d from par.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 size.d from size.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 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
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c CConverters.c -o CConverters.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c CommandLineArgs.c -o CommandLineArgs.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c Rdynload.c -o Rdynload.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c Renviron.c -o Renviron.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c RNG.c -o RNG.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c agrep.c -o agrep.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c apply.c -o apply.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c arithmetic.c -o arithmetic.o
RNG.c:443:17: warning: comparison of constant -1 with expression of type 'RNGtype' is always false [-Wtautological-constant-out-of-range-compare]
    if (newkind == -1) newkind = RNG_DEFAULT;
        ~~~~~~~ ^  ~~
RNG.c:467:14: warning: comparison of constant -1 with expression of type 'N01type' is always false [-Wtautological-constant-out-of-range-compare]
    if (kind == -1) kind = N01_DEFAULT;
        ~~~~ ^  ~~
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c array.c -o array.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c attrib.c -o attrib.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c base.c -o base.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c bind.c -o bind.o
2 warnings generated.
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c builtin.c -o builtin.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c character.c -o character.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c coerce.c -o coerce.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c colors.c -o colors.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c complex.c -o complex.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c connections.c -o connections.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c context.c -o context.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c cov.c -o cov.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c cum.c -o cum.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dcf.c -o dcf.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c datetime.c -o datetime.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c debug.c -o debug.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c deparse.c -o deparse.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c deriv.c -o deriv.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c devices.c -o devices.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dotcode.c -o dotcode.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dounzip.c -o dounzip.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dstruct.c -o dstruct.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c duplicate.c -o duplicate.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c engine.c -o engine.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c envir.c -o envir.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c errors.c -o errors.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c eval.c -o eval.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c format.c -o format.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c fourier.c -o fourier.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c gevents.c -o gevents.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c gram.c -o gram.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c gram-ex.c -o gram-ex.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c gramLatex.c -o gramLatex.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c gramRd.c -o gramRd.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c graphics.c -o graphics.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c grep.c -o grep.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c identical.c -o identical.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c inlined.c -o inlined.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c inspect.c -o inspect.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c internet.c -o internet.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c iosupport.c -o iosupport.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c lapack.c -o lapack.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c list.c -o list.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c localecharset.c -o localecharset.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c logic.c -o logic.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c main.c -o main.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c mapply.c -o mapply.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c match.c -o match.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c memory.c -o memory.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c model.c -o model.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c names.c -o names.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c objects.c -o objects.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c optim.c -o optim.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c optimize.c -o optimize.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c options.c -o options.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c par.c -o par.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c paste.c -o paste.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c platform.c -o platform.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c plot.c -o plot.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c plot3d.c -o plot3d.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c plotmath.c -o plotmath.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c print.c -o print.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c printarray.c -o printarray.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c printvector.c -o printvector.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c printutils.c -o printutils.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c qsort.c -o qsort.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c random.c -o random.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c raw.c -o raw.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c registration.c -o registration.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c relop.c -o relop.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rlocale.c -o rlocale.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c saveload.c -o saveload.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c scan.c -o scan.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c seq.c -o seq.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c serialize.c -o serialize.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c size.c -o size.o
serialize.c:2657:18: warning: comparison of constant 3 with expression of type 'Rboolean' is always false [-Wtautological-constant-out-of-range-compare]
    if (compress == 3)
        ~~~~~~~~ ^  ~
serialize.c:2659:23: warning: comparison of constant 2 with expression of type 'Rboolean' is always false [-Wtautological-constant-out-of-range-compare]
    else if (compress == 2)
             ~~~~~~~~ ^  ~
serialize.c:2688:20: warning: comparison of constant 3 with expression of type 'Rboolean' is always false [-Wtautological-constant-out-of-range-compare]
    if (compressed == 3)
        ~~~~~~~~~~ ^  ~
serialize.c:2690:25: warning: comparison of constant 2 with expression of type 'Rboolean' is always false [-Wtautological-constant-out-of-range-compare]
    else if (compressed == 2)
             ~~~~~~~~~~ ^  ~
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c sort.c -o sort.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c source.c -o source.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c split.c -o split.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c sprintf.c -o sprintf.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c startup.c -o startup.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c subassign.c -o subassign.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c subscript.c -o subscript.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c subset.c -o subset.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c summary.c -o summary.o
4 warnings generated.
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c sysutils.c -o sysutils.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c unique.c -o unique.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c util.c -o util.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c version.c -o version.o
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c vfonts.c -o vfonts.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c xxxpr.f -o xxxpr.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names   -single_module -multiply_defined suppress -L/sw/lib -install_name libR.dylib -compatibility_version 2.15.0  -current_version 2.15.3  -headerpad_max_install_names -o libR.dylib CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o fourier.o gevents.o gram.o gram-ex.o gramLatex.o gramRd.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 model.o names.o objects.o optim.o optimize.o options.o par.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 size.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o   ../unix/Rembedded.o ../unix/libunix.a ../appl/libappl.a ../nmath/libnmath.a    ../extra/tre/libtre.a    -framework Accelerate -L/sw/lib/gcc4.9/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1 -L/sw/lib/gcc4.9/lib -lgfortran -lquadmath -lm  -lintl -Wl,-framework -Wl,CoreFoundation -lreadline  -lpcre -llzma -lbz2 -lz -lm -liconv -licuuc -licui18n  
mkdir /sw/build.build/r-base215-2.15.3-112/R-2.15.3/bin/exec
mkdir /sw/build.build/r-base215-2.15.3-112/R-2.15.3/lib
flag-sort -r gcc -ffor-scope    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c Rmain.c -o Rmain.o
flag-sort -r gcc -ffor-scope  -L/sw/lib -o R.bin Rmain.o  ../../lib/libR.dylib 
making Rhttpd.d from Rhttpd.c
making dataentry.d from dataentry.c
making Rsock.d from Rsock.c
making devX11.d from devX11.c
making internet.d from internet.c
making rotated.d from rotated.c
making g_alab_her.d from g_alab_her.c
making Lapack.d from Lapack.c
making nanoftp.d from nanoftp.c
making g_cntrlify.d from g_cntrlify.c
making g_fontdb.d from g_fontdb.c
making nanohttp.d from nanohttp.c
making vecLibg95c.d from vecLibg95c.c
making g_her_glyph.d from g_her_glyph.c
making rbitmap.d from rbitmap.c
making sock.d from sock.c
flag-sort -r gcc -ffor-scope -I. -I../../../src/include -I../../../src/include -I/usr/X11R6/include -I/sw/include/pango-1.0 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I/sw/include/cairo -I/sw/include -I/sw/include/freetype2 -I/sw/include -I/opt/X11/include -I../../../src/library/grDevices/src/cairo -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c dataentry.c -o dataentry.o
flag-sort -r gcc -ffor-scope -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c Lapack.c -o Lapack.o
flag-sort -r gcc -ffor-scope -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c g_alab_her.c -o g_alab_her.o
making sockconn.d from sockconn.c
flag-sort -r gcc -ffor-scope -I. -I../../../src/include -I../../../src/include -I/usr/X11R6/include -I/sw/include/pango-1.0 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I/sw/include/cairo -I/sw/include -I/sw/include/freetype2 -I/sw/include -I/opt/X11/include -I../../../src/library/grDevices/src/cairo -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c devX11.c -o devX11.o
flag-sort -r gcc -ffor-scope -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c Rhttpd.c -o Rhttpd.o
flag-sort -r gcc -ffor-scope -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c vecLibg95c.c -o vecLibg95c.o
flag-sort -r gcc -ffor-scope -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c g_cntrlify.c -o g_cntrlify.o
flag-sort -r gcc -ffor-scope -I. -I../../../src/include -I../../../src/include -I/usr/X11R6/include -I/sw/include/pango-1.0 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I/sw/include/cairo -I/sw/include -I/sw/include/freetype2 -I/sw/include -I/opt/X11/include -I../../../src/library/grDevices/src/cairo -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rotated.c -o rotated.o
flag-sort -r gcc -ffor-scope -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c Rsock.c -o Rsock.o
flag-sort -r gcc -ffor-scope -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c g_fontdb.c -o g_fontdb.o
flag-sort -r gcc -ffor-scope -I. -I../../../src/include -I../../../src/include -I/usr/X11R6/include -I/sw/include/pango-1.0 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I/sw/include/cairo -I/sw/include -I/sw/include/freetype2 -I/sw/include -I/opt/X11/include -I../../../src/library/grDevices/src/cairo -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c rbitmap.c -o rbitmap.o
flag-sort -r gcc -ffor-scope -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c internet.c -o internet.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c vecLibg95f.f -o vecLibg95f.o
flag-sort -r gcc -ffor-scope -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c nanoftp.c -o nanoftp.o
flag-sort -r gcc -ffor-scope -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c g_her_glyph.c -o g_her_glyph.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names   -single_module -multiply_defined suppress -L/sw/lib -o lapack.dylib  Lapack.o vecLibg95c.o vecLibg95f.o ../../../lib/libR.dylib  -lintl -Wl,-framework -Wl,CoreFoundation -framework Accelerate -framework Accelerate -L/sw/lib/gcc4.9/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1 -L/sw/lib/gcc4.9/lib -lgfortran -lquadmath -lm
mkdir /sw/build.build/r-base215-2.15.3-112/R-2.15.3/modules
flag-sort -r gcc -ffor-scope -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c nanohttp.c -o nanohttp.o
flag-sort -r gcc -ffor-scope -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c sock.c -o sock.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names   -single_module -multiply_defined suppress -L/sw/lib -o vfonts.dylib g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o ../../../lib/libR.dylib   -lintl -Wl,-framework -Wl,CoreFoundation
nanohttp.c:1441:33: warning: while loop has empty body [-Wempty-body]
        while (RxmlNanoHTTPRecv(ctxt)) ;
                                       ^
nanohttp.c:1441:33: note: put the semicolon on a separate line to silence this warning
flag-sort -r gcc -ffor-scope -I. -I../../../src/include -I../../../src/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3   -c sockconn.c -o sockconn.o
1 warning generated.
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names   -single_module -multiply_defined suppress -L/sw/lib -o internet.dylib Rhttpd.o Rsock.o internet.o nanoftp.o nanohttp.o sock.o sockconn.o ../../../lib/libR.dylib  -lintl -Wl,-framework -Wl,CoreFoundation
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names   -single_module -multiply_defined suppress -L/sw/lib -o R_X11.dylib dataentry.o devX11.o rotated.o rbitmap.o -lSM -lICE -L/sw/lib -L/opt/X11/lib -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 -lintl -lz -lcairo -lX11 -lXext -L/usr/X11R6/lib -lX11 -lXt -lXmu  -ltiff -ljpeg -lpng -lz ../../../lib/libR.dylib   -lintl -Wl,-framework -Wl,CoreFoundation
mkdir ../../library
building system startup profile
mkdir ../../../library/base
mkdir ../../../library/base/R
building package 'base'
mkdir ../../../library/base/demo
mkdir ../../../library/base/po
building package 'tools'
mkdir ../../../library/tools
mkdir ../../../library/tools/R
mkdir ../../../library/tools/po
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c text.c -o text.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c init.c -o init.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c Rmd5.c -o Rmd5.o
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
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c md5.c -o md5.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c signals.c -o signals.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o tools.dylib text.o init.o Rmd5.o md5.o signals.o ../../../../lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
make[6]: `Makedeps' is up to date.
mkdir ../../../../library/tools/libs
building package 'compiler'
mkdir ../../../library/compiler
mkdir ../../../library/compiler/R
mkdir ../../../library/compiler/po
byte-compiling package 'compiler'
byte-compiling package 'base'
byte-compiling package 'tools'
building package 'utils'
mkdir ../../../library/utils
mkdir ../../../library/utils/doc
mkdir ../../../library/utils/R
mkdir ../../../library/utils/po
mkdir ../../../library/utils/Sweave
mkdir ../../../library/utils/misc
byte-compiling package 'utils'
building package 'grDevices'
mkdir ../../../library/grDevices
mkdir ../../../library/grDevices/R
mkdir ../../../library/grDevices/po
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 devCairo.d from devCairo.c
making devNull.d from devNull.c
making devPicTeX.d from devPicTeX.c
making devPS.d from devPS.c
making devQuartz.d from devQuartz.c
making init.d from init.c
making qdBitmap.d from qdBitmap.c
making qdPDF.d from qdPDF.c
making qdCocoa.d from qdCocoa.m
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/sw/include    -fPIC  -g -O3  -c axis_scales.c -o axis_scales.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/sw/include    -fPIC  -g -O3  -c chull.c -o chull.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/sw/include    -fPIC  -g -O3  -c devCairo.c -o devCairo.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/sw/include    -fPIC  -g -O3  -c devNull.c -o devNull.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/sw/include    -fPIC  -g -O3  -c devPicTeX.c -o devPicTeX.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/sw/include    -fPIC  -g -O3  -c devPS.c -o devPS.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/sw/include    -fPIC  -g -O3  -c devQuartz.c -o devQuartz.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/sw/include    -fPIC  -g -O3  -c init.c -o init.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/sw/include    -fPIC  -g -O3  -c qdBitmap.c -o qdBitmap.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/sw/include    -fPIC  -g -O3  -c qdPDF.c -o qdPDF.o
gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/sw/include   -fPIC  -g -O2 -fobjc-exceptions  -c qdCocoa.m -o qdCocoa.o
devQuartz.c:637:23: warning: 'ATSFontFindFromName' is deprecated: first deprecated in OS X 10.8 - Use CTFontCreateWithName() [-Wdeprecated-declarations]
            atsFont = ATSFontFindFromName(cfFontName, kATSOptionFlagsDefault);
                      ^
/System/Library/Frameworks/ApplicationServices.framework/Frameworks/ATS.framework/Headers/ATSFont.h:803:1: note: 'ATSFontFindFromName' declared here
ATSFontFindFromName(
^
devQuartz.c:639:27: warning: 'ATSFontFindFromPostScriptName' is deprecated: first deprecated in OS X 10.8 - Use CTFontCreateWithName() [-Wdeprecated-declarations]
                atsFont = ATSFontFindFromPostScriptName(cfFontName, kATSOptionFlagsDefault);
                          ^
/System/Library/Frameworks/ApplicationServices.framework/Frameworks/ATS.framework/Headers/ATSFont.h:820:1: note: 'ATSFontFindFromPostScriptName' declared here
ATSFontFindFromPostScriptName(
^
devQuartz.c:666:27: warning: 'ATSFontFindFromName' is deprecated: first deprecated in OS X 10.8 - Use CTFontCreateWithName() [-Wdeprecated-declarations]
                atsFont = ATSFontFindFromName(cfFontName, kATSOptionFlagsDefault);
                          ^
/System/Library/Frameworks/ApplicationServices.framework/Frameworks/ATS.framework/Headers/ATSFont.h:803:1: note: 'ATSFontFindFromName' declared here
ATSFontFindFromName(
^
devQuartz.c:667:41: warning: 'ATSFontFindFromPostScriptName' is deprecated: first deprecated in OS X 10.8 - Use CTFontCreateWithName() [-Wdeprecated-declarations]
                if (!atsFont) atsFont = ATSFontFindFromPostScriptName(cfFontName, kATSOptionFlagsDefault);
                                        ^
/System/Library/Frameworks/ApplicationServices.framework/Frameworks/ATS.framework/Headers/ATSFont.h:820:1: note: 'ATSFontFindFromPostScriptName' declared here
ATSFontFindFromPostScriptName(
^
devQuartz.c:673:35: warning: 'ATSFontFindFromName' is deprecated: first deprecated in OS X 10.8 - Use CTFontCreateWithName() [-Wdeprecated-declarations]
                        atsFont = ATSFontFindFromName(cfFontName, kATSOptionFlagsDefault);
                                  ^
/System/Library/Frameworks/ApplicationServices.framework/Frameworks/ATS.framework/Headers/ATSFont.h:803:1: note: 'ATSFontFindFromName' declared here
ATSFontFindFromName(
^
devQuartz.c:679:39: warning: 'ATSFontFindFromName' is deprecated: first deprecated in OS X 10.8 - Use CTFontCreateWithName() [-Wdeprecated-declarations]
                            atsFont = ATSFontFindFromName(cfFontName, kATSOptionFlagsDefault);
                                      ^
/System/Library/Frameworks/ApplicationServices.framework/Frameworks/ATS.framework/Headers/ATSFont.h:803:1: note: 'ATSFontFindFromName' declared here
ATSFontFindFromName(
^
devQuartz.c:687:35: warning: 'ATSFontFindFromName' is deprecated: first deprecated in OS X 10.8 - Use CTFontCreateWithName() [-Wdeprecated-declarations]
                        atsFont = ATSFontFindFromName(cfFontName, kATSOptionFlagsDefault);
                                  ^
/System/Library/Frameworks/ApplicationServices.framework/Frameworks/ATS.framework/Headers/ATSFont.h:803:1: note: 'ATSFontFindFromName' declared here
ATSFontFindFromName(
^
devQuartz.c:706:12: warning: 'CGFontCreateWithPlatformFont' is deprecated: first deprecated in OS X 10.6 [-Wdeprecated-declarations]
    return CGFontCreateWithPlatformFont(&atsFont);
           ^
/System/Library/Frameworks/CoreGraphics.framework/Headers/CGFont.h:61:21: note: 'CGFontCreateWithPlatformFont' declared here
CG_EXTERN CGFontRef CGFontCreateWithPlatformFont(void *platformFontReference)
                    ^
devQuartz.c:991:5: warning: 'CGContextShowGlyphsWithAdvances' is deprecated: first deprecated in OS X 10.9 [-Wdeprecated-declarations]
    CGContextShowGlyphsWithAdvances(ctx,glyphs, g_adv, len);
    ^
/System/Library/Frameworks/CoreGraphics.framework/Headers/CGContext.h:1023:16: note: 'CGContextShowGlyphsWithAdvances' declared here
CG_EXTERN void CGContextShowGlyphsWithAdvances(CGContextRef context,
               ^
qdCocoa.m:99:23: warning: sending 'QuartzCocoaView *' to parameter of incompatible type 'id<NSWindowDelegate>'
        [window setDelegate: view];
                             ^~~~
/System/Library/Frameworks/AppKit.framework/Headers/NSWindow.h:319:44: note: passing argument to parameter 'anObject' here
- (void)setDelegate:(id <NSWindowDelegate>)anObject;
                                           ^
qdCocoa.m:266:6: warning: 'setRequiredFileType:' is deprecated: first deprecated in OS X 10.6 [-Wdeprecated-declarations]
        [sp setRequiredFileType:@"pdf"];
            ^
/System/Library/Frameworks/AppKit.framework/Headers/NSSavePanel.h:305:1: note: method 'setRequiredFileType:' declared here
- (void)setRequiredFileType:(NSString *)type NS_DEPRECATED_MAC(10_0, 10_6);
^
qdCocoa.m:268:19: warning: 'runModalForDirectory:file:' is deprecated: first deprecated in OS X 10.6 [-Wdeprecated-declarations]
        int answer = [sp runModalForDirectory:nil file:@"Rplot.pdf"];
                         ^
/System/Library/Frameworks/AppKit.framework/Headers/NSSavePanel.h:313:1: note: method 'runModalForDirectory:file:' declared here
- (NSInteger)runModalForDirectory:(NSString *)path file:(NSString *)name NS_DEPRECATED_MAC(10_0, 10_6);
^
qdCocoa.m:270:29: warning: 'filename' is deprecated: first deprecated in OS X 10.6 [-Wdeprecated-declarations]
                if (![self writeAsPDF:[sp filename]]) NSBeep();
                                          ^
/System/Library/Frameworks/AppKit.framework/Headers/NSSavePanel.h:295:1: note: method 'filename' declared here
- (NSString *)filename NS_DEPRECATED_MAC(10_0, 10_6);
^
qdCocoa.m:613:13: warning: 'GetFrontProcess' is deprecated: first deprecated in OS X 10.9 [-Wdeprecated-declarations]
        if (GetFrontProcess(&frProc) == noErr) {
            ^
/System/Library/Frameworks/ApplicationServices.framework/Frameworks/HIServices.framework/Headers/Processes.h:434:1: note: 'GetFrontProcess' declared here
GetFrontProcess(ProcessSerialNumber * PSN)                    AVAILABLE_MAC_OS_X_VERSION_10_0_AND_LATER_BUT_DEPRECATED_IN_MAC_OS_X_VERSION_10_9;
^
qdCocoa.m:614:17: warning: 'GetCurrentProcess' is deprecated: first deprecated in OS X 10.9 [-Wdeprecated-declarations]
            if (GetCurrentProcess(&myProc) == noErr) {
                ^
/System/Library/Frameworks/ApplicationServices.framework/Frameworks/HIServices.framework/Headers/Processes.h:415:1: note: 'GetCurrentProcess' declared here
MacGetCurrentProcess(ProcessSerialNumber * PSN)               AVAILABLE_MAC_OS_X_VERSION_10_0_AND_LATER_BUT_DEPRECATED_IN_MAC_OS_X_VERSION_10_9;
^
/System/Library/Frameworks/ApplicationServices.framework/Frameworks/HIServices.framework/Headers/Processes.h:412:34: note: expanded from macro 'MacGetCurrentProcess'
    #define MacGetCurrentProcess GetCurrentProcess
                                 ^
qdCocoa.m:615:21: warning: 'SameProcess' is deprecated: first deprecated in OS X 10.9 [-Wdeprecated-declarations]
                if (SameProcess(&frProc, &myProc, &sameProc) == noErr && !sameProc) {
                    ^
/System/Library/Frameworks/ApplicationServices.framework/Frameworks/HIServices.framework/Headers/Processes.h:696:1: note: 'SameProcess' declared here
SameProcess(
^
qdCocoa.m:618:17: warning: 'SetFrontProcess' is deprecated: first deprecated in OS X 10.9 [-Wdeprecated-declarations]
                SetFrontProcess(&myProc);
                ^
/System/Library/Frameworks/ApplicationServices.framework/Frameworks/HIServices.framework/Headers/Processes.h:603:1: note: 'SetFrontProcess' declared here
SetFrontProcess(const ProcessSerialNumber * PSN)              AVAILABLE_MAC_OS_X_VERSION_10_0_AND_LATER_BUT_DEPRECATED_IN_MAC_OS_X_VERSION_10_9;
^
9 warnings generated.
8 warnings generated.
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o grDevices.dylib axis_scales.o chull.o devCairo.o devNull.o devPicTeX.o devPS.o devQuartz.o init.o qdBitmap.o qdPDF.o qdCocoa.o -framework AppKit -lz ../../../../lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
make[6]: `Makedeps' is up to date.
mkdir ../../../../library/grDevices/libs
making cairoBM.d from cairoBM.c
make[8]: `Makedeps' is up to date.
flag-sort -r gcc -ffor-scope -I. -I../../../../../src/include -I../../../../../src/include -I/sw/include/pango-1.0 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I/sw/include/cairo -I/sw/include -I/sw/include/freetype2 -I/sw/include -I/opt/X11/include -I../../../../../src/modules/X11 -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -c cairoBM.c -o cairoBM.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names   -single_module -multiply_defined suppress -L/sw/lib -o cairo.dylib cairoBM.o ../../../../../src/modules/X11/rbitmap.o -L/sw/lib -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 -lintl -lz -lcairo -ltiff -ljpeg -lpng -lz ../../../../../lib/libR.dylib   -lintl -Wl,-framework -Wl,CoreFoundation
byte-compiling package 'grDevices'
building package 'graphics'
mkdir ../../../library/graphics
mkdir ../../../library/graphics/R
mkdir ../../../library/graphics/po
byte-compiling package 'graphics'
building package 'stats'
mkdir ../../../library/stats
mkdir ../../../library/stats/R
mkdir ../../../library/stats/po
making init.d from init.c
making kmeans.d from kmeans.c
making ansari.d from ansari.c
making bandwidths.d from bandwidths.c
making chisqsim.d from chisqsim.c
making d2x2xk.d from d2x2xk.c
making fexact.d from fexact.c
making kendall.d from kendall.c
making ks.d from ks.c
making line.d from line.c
making smooth.d from smooth.c
making prho.d from prho.c
making swilk.d from swilk.c
making ksmooth.d from ksmooth.c
making loessc.d from loessc.c
making monoSpl.d from monoSpl.c
making isoreg.d from isoreg.c
making Srunmed.d from Srunmed.c
making Trunmed.d from Trunmed.c
making dblcen.d from dblcen.c
making distance.d from distance.c
making hclust-utils.d from hclust-utils.c
making nls.d from nls.c
making rWishart.d from rWishart.c
making HoltWinters.d from HoltWinters.c
making PPsum.d from PPsum.c
making arima.d from arima.c
making burg.d from burg.c
making filter.d from filter.c
making mAR.d from mAR.c
making pacf.d from pacf.c
making starma.d from starma.c
making port.d from port.c
making family.d from family.c
making sbart.d from sbart.c
making approx.d from approx.c
making loglin.d from loglin.c
making lowess.d from lowess.c
making massdist.d from massdist.c
making splines.d from splines.c
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c init.c -o init.o
making lm.d from lm.c
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c kmeans.c -o kmeans.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c ansari.c -o ansari.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c bandwidths.c -o bandwidths.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c chisqsim.c -o chisqsim.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c d2x2xk.c -o d2x2xk.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c fexact.c -o fexact.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c kendall.c -o kendall.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c ks.c -o ks.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c line.c -o line.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c smooth.c -o smooth.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c prho.c -o prho.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c swilk.c -o swilk.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c ksmooth.c -o ksmooth.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c loessc.c -o loessc.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c monoSpl.c -o monoSpl.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c isoreg.c -o isoreg.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c Srunmed.c -o Srunmed.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c Trunmed.c -o Trunmed.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c dblcen.c -o dblcen.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c distance.c -o distance.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c hclust-utils.c -o hclust-utils.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c nls.c -o nls.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c rWishart.c -o rWishart.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c HoltWinters.c -o HoltWinters.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c PPsum.c -o PPsum.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c arima.c -o arima.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c burg.c -o burg.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c filter.c -o filter.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c mAR.c -o mAR.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c pacf.c -o pacf.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c starma.c -o starma.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c port.c -o port.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c family.c -o family.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c sbart.c -o sbart.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c approx.c -o approx.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c loglin.c -o loglin.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c lowess.c -o lowess.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c massdist.c -o massdist.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c splines.c -o splines.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c lm.c -o lm.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c bsplvd.f -o bsplvd.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c bvalue.f -o bvalue.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c bvalus.f -o bvalus.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c loessf.f -o loessf.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c ppr.f -o ppr.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c qsbart.f -o qsbart.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c sgram.f -o sgram.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c sinerp.f -o sinerp.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c sslvrg.f -o sslvrg.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c stxwx.f -o stxwx.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c hclust.f -o hclust.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c kmns.f -o kmns.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c eureka.f -o eureka.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c stl.f -o stl.o
/sw/bin/gfortran-fsf-4.9 -fPIC  -g -O3 -ffloat-store -c portsrc.f -o portsrc.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c lminfl.f -o lminfl.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o stats.dylib init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o Trunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -framework Accelerate -framework Accelerate -L/sw/lib/gcc4.9/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1 -L/sw/lib/gcc4.9/lib -lgfortran -lquadmath -lm ../../../../lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
ld: warning: ld: warning: could not create compact unwind for _spline_: stack subq instruction is too different from dwarf stack sizecould not create compact unwind for _ehg136_: stack subq instruction is too different from dwarf stack size

ld: warning: could not create compact unwind for _ehg139_: stack subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _dg7itb_: stack subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _dg7lit_: stack subq instruction is too different from dwarf stack size
make[6]: `Makedeps' is up to date.
mkdir ../../../../library/stats/libs
byte-compiling package 'stats'
building package 'datasets'
mkdir ../../../library/datasets
mkdir ../../../library/datasets/data
building package 'methods'
mkdir ../../../library/methods
mkdir ../../../library/methods/R
mkdir ../../../library/methods/po
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c do_substitute_direct.c -o do_substitute_direct.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c init.c -o init.o
making do_substitute_direct.d from do_substitute_direct.c
making init.d from init.c
making methods_list_dispatch.d from methods_list_dispatch.c
making slot.d from slot.c
making class_support.d from class_support.c
making tests.d from tests.c
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c methods_list_dispatch.c -o methods_list_dispatch.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c slot.c -o slot.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c class_support.c -o class_support.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/sw/include    -fPIC  -g -O3  -c tests.c -o tests.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o methods.dylib do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o ../../../../lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
make[6]: `Makedeps' is up to date.
mkdir ../../../../library/methods/libs
byte-compiling 'methods'
initializing class and method definitions ...
done
building package 'grid'
mkdir ../../../library/grid
mkdir ../../../library/grid/doc
mkdir ../../../library/grid/R
mkdir ../../../library/grid/po
making gpar.d from gpar.c
making grid.d from grid.c
making just.d from just.c
making layout.d from layout.c
making matrix.d from matrix.c
making register.d from register.c
making state.d from state.c
making unit.d from unit.c
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c gpar.c -o gpar.o
making util.d from util.c
making viewport.d from viewport.c
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c grid.c -o grid.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c just.c -o just.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c layout.c -o layout.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c matrix.c -o matrix.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c register.c -o register.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c state.c -o state.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c unit.c -o unit.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c util.c -o util.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c viewport.c -o viewport.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o grid.dylib gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o ../../../../lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
make[6]: `Makedeps' is up to date.
mkdir ../../../../library/grid/libs
byte-compiling package 'grid'
building package 'splines'
mkdir ../../../library/splines
mkdir ../../../library/splines/R
mkdir ../../../library/splines/po
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c splines.c -o splines.o
making splines.d from splines.c
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o splines.dylib splines.o ../../../../lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
make[6]: `Makedeps' is up to date.
mkdir ../../../../library/splines/libs
byte-compiling package 'splines'
building package 'stats4'
mkdir ../../../library/stats4
mkdir ../../../library/stats4/R
mkdir ../../../library/stats4/po
byte-compiling package 'stats4'
building package 'tcltk'
mkdir ../../../library/tcltk
mkdir ../../../library/tcltk/R
mkdir ../../../library/tcltk/po
mkdir ../../../library/tcltk/exec
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I/sw/include -I/sw/include -I/usr/X11R6/include -I/sw/include    -fPIC  -g -O3  -c init.c -o init.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I/sw/include -I/sw/include -I/usr/X11R6/include -I/sw/include    -fPIC  -g -O3  -c tcltk.c -o tcltk.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG -I/sw/include -I/sw/include -I/usr/X11R6/include -I/sw/include    -fPIC  -g -O3  -c tcltk_unix.c -o tcltk_unix.o
making tcltk_unix.d from tcltk_unix.c
making init.d from init.c
making tcltk.d from tcltk.c
In file included from tcltk_unix.c:23:
../../../../include/R_ext/eventloop.h:79:35: warning: declaration of 'struct timeval' will not be visible outside of this function [-Wvisibility]
                      fd_set *exceptfds, struct timeval *timeout,
                                                ^
1 warning generated.
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o tcltk.dylib init.o tcltk.o tcltk_unix.o -L/sw/lib -ltcl8.6 -L/sw/lib -ltk8.6 -L/usr/X11R6/lib -lX11 -Wl,-weak-lXss -lXext ../../../../lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
make[5]: `Makedeps' is up to date.
mkdir ../../../../library/tcltk/libs
byte-compiling package 'tcltk'
building package 'parallel'
mkdir ../../../library/parallel
mkdir ../../../library/parallel/doc
mkdir ../../../library/parallel/R
mkdir ../../../library/parallel/po
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c init.c -o init.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c rngstream.c -o rngstream.o
flag-sort -r gcc -ffor-scope -I../../../../include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c fork.c -o fork.o
making init.d from init.c
making rngstream.d from rngstream.c
making fork.d from fork.c
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o parallel.dylib init.o rngstream.o fork.o ../../../../lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
make[6]: `Makedeps' is up to date.
mkdir ../../../../library/parallel/libs
byte-compiling package 'parallel'
installing parsed NAMESPACE files
make[1]: Nothing to be done for `R'.
installing translations:
mkdir ../share/locale
mkdir ../share/locale/da
mkdir ../share/locale/da/LC_MESSAGES
  da
mkdir ../share/locale/en
mkdir ../share/locale/en/LC_MESSAGES
  en
mkdir ../share/locale/en_GB
mkdir ../share/locale/en_GB/LC_MESSAGES
  en_GB
mkdir ../share/locale/es
mkdir ../share/locale/es/LC_MESSAGES
  es
mkdir ../share/locale/fr
mkdir ../share/locale/fr/LC_MESSAGES
  fr
mkdir ../share/locale/de
mkdir ../share/locale/de/LC_MESSAGES
  de
mkdir ../share/locale/it
mkdir ../share/locale/it/LC_MESSAGES
  it
mkdir ../share/locale/ja
mkdir ../share/locale/ja/LC_MESSAGES
  ja
mkdir ../share/locale/ko
mkdir ../share/locale/ko/LC_MESSAGES
  ko
mkdir ../share/locale/nn
mkdir ../share/locale/nn/LC_MESSAGES
  nn
mkdir ../share/locale/pl
mkdir ../share/locale/pl/LC_MESSAGES
  pl
mkdir ../share/locale/pt_BR
mkdir ../share/locale/pt_BR/LC_MESSAGES
  pt_BR
mkdir ../share/locale/ru
mkdir ../share/locale/ru/LC_MESSAGES
  ru
mkdir ../share/locale/tr
mkdir ../share/locale/tr/LC_MESSAGES
  tr
mkdir ../share/locale/zh_CN
mkdir ../share/locale/zh_CN/LC_MESSAGES
  zh_CN
mkdir ../share/locale/zh_TW
mkdir ../share/locale/zh_TW/LC_MESSAGES
  zh_TW
mkdir ../share/locale/en@quot
mkdir ../share/locale/en@quot/LC_MESSAGES
  en@quot
you should 'make docs' now ...
creating NEWS
'pdflatex' is needed to make NEWS.pdf but is missing on your system.
creating doc/manual/R-FAQ.html
creating doc/manual/version.texi
creating doc/manual/R-admin.html
creating doc/manual/R-data.html
creating doc/manual/R-exts.html
creating doc/manual/R-intro.html
creating doc/manual/R-ints.html
creating doc/manual/R-lang.html
installing parsed Rd
  datasets
  grid
  grDevices
  tcltk
  splines
  graphics
  compiler
  methods
  stats4
  tools
  parallel
  utils
  stats
  base
building/updating package metadata ...
writing package indices
begin installing recommended package MASS
begin installing recommended package lattice
begin installing recommended package survival
begin installing recommended package codetools
begin installing recommended package foreign
begin installing recommended package KernSmooth
begin installing recommended package rpart
begin installing recommended package nnet
* installing *source* package 'codetools' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (codetools)
* installing *source* package 'nnet' ...
** libs
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c nnet.c -o nnet.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o nnet.dylib nnet.o /sw/build.build/r-base215-2.15.3-112/R-2.15.3/lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
installing to /sw/build.build/r-base215-2.15.3-112/R-2.15.3/library/nnet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (nnet)
begin installing recommended package spatial
* installing *source* package 'KernSmooth' ...
** package 'KernSmooth' successfully unpacked and MD5 sums checked
** libs
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c blkest.f -o blkest.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c cp.f -o cp.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dgedi.f -o dgedi.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dgefa.f -o dgefa.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dgesl.f -o dgesl.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c init.c -o init.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c linbin.f -o linbin.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c linbin2D.f -o linbin2D.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c locpoly.f -o locpoly.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c rlbin.f -o rlbin.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c sdiag.f -o sdiag.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c sstdiag.f -o sstdiag.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o KernSmooth.dylib blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -framework Accelerate -L/sw/lib/gcc4.9/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1 -L/sw/lib/gcc4.9/lib -lgfortran -lquadmath -lm -L/sw/lib/gcc4.9/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1 -L/sw/lib/gcc4.9/lib -lgfortran -lquadmath -lm /sw/build.build/r-base215-2.15.3-112/R-2.15.3/lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
installing to /sw/build.build/r-base215-2.15.3-112/R-2.15.3/library/KernSmooth/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (KernSmooth)
* installing *source* package 'spatial' ...
** libs
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c init.c -o init.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c krc.c -o krc.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c pps.c -o pps.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o spatial.dylib init.o krc.o pps.o /sw/build.build/r-base215-2.15.3-112/R-2.15.3/lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
installing to /sw/build.build/r-base215-2.15.3-112/R-2.15.3/library/spatial/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (spatial)
* installing *source* package 'foreign' ...
** libs
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c R_systat.c -o R_systat.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c Rdbfread.c -o Rdbfread.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c Rdbfwrite.c -o Rdbfwrite.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c SASxport.c -o SASxport.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c avl.c -o avl.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c dbfopen.c -o dbfopen.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c file-handle.c -o file-handle.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c format.c -o format.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c init.c -o init.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c minitab.c -o minitab.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c pfm-read.c -o pfm-read.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c sfm-read.c -o sfm-read.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c spss.c -o spss.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c stataread.c -o stataread.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o foreign.dylib R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o /sw/build.build/r-base215-2.15.3-112/R-2.15.3/lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
installing to /sw/build.build/r-base215-2.15.3-112/R-2.15.3/library/foreign/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (foreign)
* installing *source* package 'rpart' ...
** libs
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c anova.c -o anova.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c anovapred.c -o anovapred.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c branch.c -o branch.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c bsplit.c -o bsplit.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c choose_surg.c -o choose_surg.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c fix_cp.c -o fix_cp.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c free_tree.c -o free_tree.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c gini.c -o gini.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c graycode.c -o graycode.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c init.c -o init.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c insert_split.c -o insert_split.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c make_cp_list.c -o make_cp_list.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c make_cp_table.c -o make_cp_table.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c mysort.c -o mysort.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c nodesplit.c -o nodesplit.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c partition.c -o partition.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c poisson.c -o poisson.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c pred_rpart.c -o pred_rpart.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c print_tree.c -o print_tree.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c rpart.c -o rpart.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c rpart_callback.c -o rpart_callback.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c rpartexp.c -o rpartexp.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c rpartexp2.c -o rpartexp2.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c rpcountup.c -o rpcountup.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c rpmatrix.c -o rpmatrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c rundown.c -o rundown.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c rundown2.c -o rundown2.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c surrogate.c -o surrogate.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c usersplit.c -o usersplit.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c xpred.c -o xpred.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c xval.c -o xval.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o rpart.dylib anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o /sw/build.build/r-base215-2.15.3-112/R-2.15.3/lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
installing to /sw/build.build/r-base215-2.15.3-112/R-2.15.3/library/rpart/libs
** R
** data
**  moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'longintro.Rnw' 
   'usercode.Rnw' 
** testing if installed package can be loaded

* DONE (rpart)
* installing *source* package 'MASS' ...
** libs
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c MASS.c -o MASS.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c lqs.c -o lqs.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o MASS.dylib MASS.o lqs.o /sw/build.build/r-base215-2.15.3-112/R-2.15.3/lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
installing to /sw/build.build/r-base215-2.15.3-112/R-2.15.3/library/MASS/libs
** R
** data
**  moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (MASS)
begin installing recommended package cluster
begin installing recommended package class
* installing *source* package 'class' ...
** libs
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c class.c -o class.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o class.dylib class.o /sw/build.build/r-base215-2.15.3-112/R-2.15.3/lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
installing to /sw/build.build/r-base215-2.15.3-112/R-2.15.3/library/class/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (class)
* installing *source* package 'lattice' ...
** libs
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c init.c -o init.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c threeDplot.c -o threeDplot.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o lattice.dylib init.o threeDplot.o /sw/build.build/r-base215-2.15.3-112/R-2.15.3/lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
installing to /sw/build.build/r-base215-2.15.3-112/R-2.15.3/library/lattice/libs
** R
** data
**  moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (lattice)
begin installing recommended package Matrix
begin installing recommended package nlme
* installing *source* package 'cluster' ...
** libs
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c clara.c -o clara.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c daisy.f -o daisy.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c dysta.f -o dysta.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c fanny.c -o fanny.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c init.c -o init.o
/sw/bin/gfortran-fsf-4.9   -fPIC  -g -O3  -c mona.f -o mona.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c pam.c -o pam.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c sildist.c -o sildist.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c spannel.c -o spannel.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c twins.c -o twins.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o cluster.dylib clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -L/sw/lib/gcc4.9/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1 -L/sw/lib/gcc4.9/lib -lgfortran -lquadmath -lm /sw/build.build/r-base215-2.15.3-112/R-2.15.3/lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
installing to /sw/build.build/r-base215-2.15.3-112/R-2.15.3/library/cluster/libs
** R
** data
**  moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (cluster)
* installing *source* package 'survival' ...
** libs
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c agexact.c -o agexact.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c agfit3.c -o agfit3.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c agfit5.c -o agfit5.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c agmart.c -o agmart.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c agmart2.c -o agmart2.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c agscore.c -o agscore.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c agsurv3.c -o agsurv3.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c agsurv4.c -o agsurv4.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c agsurv5.c -o agsurv5.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c chinv2.c -o chinv2.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c chinv3.c -o chinv3.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c cholesky2.c -o cholesky2.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c cholesky3.c -o cholesky3.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c chsolve2.c -o chsolve2.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c chsolve3.c -o chsolve3.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c concordance1.c -o concordance1.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c cox_Rcallback.c -o cox_Rcallback.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c coxcount1.c -o coxcount1.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c coxdetail.c -o coxdetail.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c coxexact.c -o coxexact.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c coxfit2.c -o coxfit2.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c coxfit5.c -o coxfit5.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c coxfit6.c -o coxfit6.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c coxmart.c -o coxmart.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c coxmart2.c -o coxmart2.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c coxph_wtest.c -o coxph_wtest.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c coxsafe.c -o coxsafe.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c coxscho.c -o coxscho.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c coxscore.c -o coxscore.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c dmatrix.c -o dmatrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c doloop.c -o doloop.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c msurv.c -o msurv.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c pyears1.c -o pyears1.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c pyears2.c -o pyears2.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c pyears3b.c -o pyears3b.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c pystep.c -o pystep.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c survConcordance.c -o survConcordance.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c survdiff2.c -o survdiff2.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c survfit4.c -o survfit4.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c survfitci.c -o survfitci.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c survpenal.c -o survpenal.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c survreg6.c -o survreg6.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c survreg7.c -o survreg7.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c survregc1.c -o survregc1.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c survregc2.c -o survregc2.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o survival.dylib agexact.o agfit3.o agfit5.o agmart.o agmart2.o agscore.o agsurv3.o agsurv4.o agsurv5.o chinv2.o chinv3.o cholesky2.o cholesky3.o chsolve2.o chsolve3.o concordance1.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit2.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore.o dmatrix.o doloop.o msurv.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o /sw/build.build/r-base215-2.15.3-112/R-2.15.3/lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
installing to /sw/build.build/r-base215-2.15.3-112/R-2.15.3/library/survival/libs
** R
** data
**  moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'timedep.Rnw' 
** testing if installed package can be loaded

* DONE (survival)
begin installing recommended package boot
* installing *source* package 'boot' ...
** R
** data
**  moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (boot)
* installing *source* package 'nlme' ...
** libs
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c corStruct.c -o corStruct.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c gnls.c -o gnls.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c init.c -o init.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c matrix.c -o matrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c nlOptimizer.c -o nlOptimizer.o
In file included from gnls.cmatrix.cinit.c::25:
./nlOptim:5er.h::235ile included from corStruct.c::
5./:9Optimizer.h:.2 atrix.h:w23ning: :99matrix.h:: w:rning: '23arningPTIMIZER_H' is used as a header guard here, followed by #define of a different macro [-Wheader-gua
d]: '9LME_NLOPTIMIZER_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
: warning: 'NLME_MATRIX_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef NLME_MATRIX_H#        ^~~~~~~~~~~~~ER_H

 #ifndef NLME_NLOPTIMIZER_H

        ^~~~~~~~~~~~~~~~~~
#ifndef NLME_MATRIX_H
        ^~~~~~~~~~~~~
./matrix.h.24lOptimizer.h::29nlOptimizer.h::29:.9 atrix.h::n24:: note: : 'NLME_MATRIC_H' is defined here; did you mean 'NLME_MATRIX_H'?
'N'N:ME_NL_OPTIMIZER_H' is defined here; did you mean 'NLME_NLOPTIMIZER_H'?

#de:ine NLME_MATRIC_H
  note   ^~~~~~~~~~~~~
:  #define NLME_NL_OPTIMIZER_He NLME_NL_OPTIMIZER_HLME_MATRIX_H'?


 #define NLME_MATRIC_H~~~~~~


        NLME_NLOPTIMIZE        NLME_NLOPTIMIZER_H


In file included from gnls.c:26:
./matrix.h:23:9: warning: 'NLME_MATRIX_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef NLME_MATRIX_H
        ^~~~~~~~~~~~~
./matrix.h:24:9: note: 'NLME_MATRIC_H' is defined here; did you mean 'NLME_MATRIX_H'?
#define NLME_MATRIC_H
        ^~~~~~~~~~~~~
        NLME_MATRIX_H
In file included from nlOptimizer.c:23:
./nlOptimizer.h:23:9: warning: 'NLME_NLOPTIMIZER_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef NLME_NLOPTIMIZER_H
        ^~~~~~~~~~~~~~~~~~
./nlOptimizer.h:24:9: note: 'NLME_NL_OPTIMIZER_H' is defined here; did you mean 'NLME_NLOPTIMIZER_H'?
#define NLME_NL_OPTIMIZER_H
        ^~~~~~~~~~~~~~~~~~~
        NLME_NLOPTIMIZER_H
1 warning generated.
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c nlme.c -o nlme.o
1 warning generated.
2 warnings generated.
1 warning generated.
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c nlmefit.c -o nlmefit.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c nls.c -o nls.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c pdMat.c -o pdMat.o
In file included from nlme.c:25:
./nlOptimizer.h:23:9: warning: 'NLME_NLOPTIMIZER_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef NLME_NLOPTIMIZER_H
        ^~~~~~~~~~~~~~~~~~
./nlOptimizer.h:24:9: note: 'NLME_NL_OPTIMIZER_H' is defined here; did you mean 'NLME_NLOPTIMIZER_H'?
#define NLME_NL_OPTIMIZER_H
        ^~~~~~~~~~~~~~~~~~~
        NLME_NLOPTIMIZER_H
In file included from nlme.c:26:
./matrix.h:23:9: warning: 'NLME_MATRIX_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef NLME_MATRIX_H
        ^~~~~~~~~~~~~
./matrix.h:24:9: note: 'NLME_MATRIC_H' is defined here; did you mean 'NLME_MATRIX_H'?
#define NLME_MATRIC_H
        ^~~~~~~~~~~~~
        NLME_MATRIX_H
In file included from nlmefit.c:27:
./matrix.h:23:9: warning: 'NLME_MATRIX_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef NLME_MATRIX_H
        ^~~~~~~~~~~~~
./matrix.h:24:9: note: 'NLME_MATRIC_H' is defined here; did you mean 'NLME_MATRIX_H'?
#define NLME_MATRIC_H
        ^~~~~~~~~~~~~
        NLME_MATRIX_H
In file included from pdMat.c:26:
./matrix.h:23:9: warning: 'NLME_MATRIX_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef NLME_MATRIX_H
        ^~~~~~~~~~~~~
./matrix.h:24:9: note: 'NLME_MATRIC_H' is defined here; did you mean 'NLME_MATRIX_H'?
#define NLME_MATRIC_H
        ^~~~~~~~~~~~~
        NLME_MATRIX_H
1 warning generated.
2 warnings generated.
1 warning generated.
1 warning generated.
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o nlme.dylib corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o nls.o pdMat.o /sw/build.build/r-base215-2.15.3-112/R-2.15.3/lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
installing to /sw/build.build/r-base215-2.15.3-112/R-2.15.3/library/nlme/libs
** R
** data
**  moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (nlme)
* installing *source* package 'Matrix' ...
** libs
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c CHMfactor.c -o CHMfactor.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c Csparse.c -o Csparse.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c TMatrix_as.c -o TMatrix_as.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c Tsparse.c -o Tsparse.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c init.c -o init.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c Mutils.c -o Mutils.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c chm_common.c -o chm_common.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c cs.c -o cs.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c cs_utils.c -o cs_utils.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c dense.c -o dense.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c dgCMatrix.c -o dgCMatrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c dgTMatrix.c -o dgTMatrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c dgeMatrix.c -o dgeMatrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c dpoMatrix.c -o dpoMatrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c dppMatrix.c -o dppMatrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c dsCMatrix.c -o dsCMatrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c dsyMatrix.c -o dsyMatrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c dspMatrix.c -o dspMatrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c dtCMatrix.c -o dtCMatrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c dtTMatrix.c -o dtTMatrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c dtrMatrix.c -o dtrMatrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c dtpMatrix.c -o dtpMatrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c factorizations.c -o factorizations.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c ldense.c -o ldense.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c lgCMatrix.c -o lgCMatrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c sparseQR.c -o sparseQR.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c abIndex.c -o abIndex.o
( cd Lib ; /Applications/Xcode.app/Contents/Developer/usr/bin/make clean )
( cd Source ; /Applications/Xcode.app/Contents/Developer/usr/bin/make clean )
( cd Source ; /Applications/Xcode.app/Contents/Developer/usr/bin/make clean )
( cd Lib ; /Applications/Xcode.app/Contents/Developer/usr/bin/make )
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Core/cholmod_aat.c -o cholmod_aat.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Core/cholmod_add.c -o cholmod_add.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Core/cholmod_band.c -o cholmod_band.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Core/cholmod_common.c -o cholmod_common.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Core/cholmod_complex.c -o cholmod_complex.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Core/cholmod_copy.c -o cholmod_copy.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Core/cholmod_dense.c -o cholmod_dense.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Core/cholmod_error.c -o cholmod_error.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Core/cholmod_factor.c -o cholmod_factor.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Core/cholmod_memory.c -o cholmod_memory.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Core/cholmod_sparse.c -o cholmod_sparse.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Core/cholmod_transpose.c -o cholmod_transpose.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Core/cholmod_triplet.c -o cholmod_triplet.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Check/cholmod_check.c -o cholmod_check.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Check/cholmod_read.c -o cholmod_read.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Check/cholmod_write.c -o cholmod_write.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Modify/cholmod_updown.c -o cholmod_updown.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Core/cholmod_aat.c -o cholmod_l_aat.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Core/cholmod_add.c -o cholmod_l_add.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Core/cholmod_band.c -o cholmod_l_band.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Core/cholmod_common.c -o cholmod_l_common.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Core/cholmod_complex.c -o cholmod_l_complex.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Core/cholmod_copy.c -o cholmod_l_copy.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Core/cholmod_dense.c -o cholmod_l_dense.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Core/cholmod_error.c -o cholmod_l_error.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Core/cholmod_factor.c -o cholmod_l_factor.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Core/cholmod_memory.c -o cholmod_l_memory.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Core/cholmod_sparse.c -o cholmod_l_sparse.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Core/cholmod_transpose.c -o cholmod_l_transpose.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Core/cholmod_triplet.c -o cholmod_l_triplet.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Check/cholmod_check.c -o cholmod_l_check.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Check/cholmod_read.c -o cholmod_l_read.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Check/cholmod_write.c -o cholmod_l_write.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Modify/cholmod_updown.c -o cholmod_l_updown.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/sw/include    -fPIC  -g -O3  -DDLONG -c  ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o
ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o  cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o 
( cd Source ; /Applications/Xcode.app/Contents/Developer/usr/bin/make lib )
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c colamd_global.c -o colamd_global.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -c colamd.c -o colamd.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDLONG -c colamd.c -o colamd_l.o
colamd_global.c:22:7: warning: incompatible pointer types initializing 'int (*)(const char *, ...)' with an expression of type 'void (const char *, ...)' [-Wincompatible-pointer-types]
int (*colamd_printf) (const char *, ...) = printf ;
      ^                                    ~~~~~~
1 warning generated.
ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o
( cd Source ; /Applications/Xcode.app/Contents/Developer/usr/bin/make lib )
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDINT -c amd_1.c -o amd_i_1.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDLONG -c amd_1.c -o amd_l_1.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDINT -c amd_2.c -o amd_i_2.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDLONG -c amd_2.c -o amd_l_2.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDINT -c amd_order.c -o amd_i_order.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDLONG -c amd_order.c -o amd_l_order.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDINT -c amd_control.c -o amd_i_control.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDLONG -c amd_control.c -o amd_l_control.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDINT -c amd_info.c -o amd_i_info.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDLONG -c amd_info.c -o amd_l_info.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDINT -c amd_global.c -o amd_i_global.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/sw/include    -fPIC  -g -O3  -I../Include -DDLONG -c amd_global.c -o amd_l_global.o
amd_global.c:81:7: warning: incompatible pointer types initializing 'int (*)(const char *, ...)' with an expression of type 'void (const char *, ...)' [-Wincompatible-pointer-types]
int (*amd_printf) (const char *, ...) = printf ;
      ^                                 ~~~~~~
1 warning generated.
amd_global.c:81:7: warning: incompatible pointer types initializing 'int (*)(const char *, ...)' with an expression of type 'void (const char *, ...)' [-Wincompatible-pointer-types]
int (*amd_printf) (const char *, ...) = printf ;
      ^                                 ~~~~~~
1 warning generated.
ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o amd_i_global.o amd_l_global.o 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../../AMD.a(amd_i_dump.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../../AMD.a(amd_l_dump.o) has no symbols
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG -DNTIMER -I/sw/include    -fPIC  -g -O3  -c SuiteSparse_config.c -o SuiteSparse_config.o
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o Matrix.dylib CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -framework Accelerate -framework Accelerate -L/sw/lib/gcc4.9/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1 -L/sw/lib/gcc4.9/lib -lgfortran -lquadmath -lm /sw/build.build/r-base215-2.15.3-112/R-2.15.3/lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
installing to /sw/build.build/r-base215-2.15.3-112/R-2.15.3/library/Matrix/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'image' from package 'graphics' in package 'Matrix'
Creating a generic function for 'solve' from package 'base' in package 'Matrix'
Creating a generic function for 'chol2inv' from 'base' in package 'Matrix'
    (from the saved implicit definition)
Creating a generic function for 'chol2inv' from package 'base' in package 'Matrix'
Creating a generic function for 'determinant' from package 'base' in package 'Matrix'
Creating a generic function for 'update' from package 'stats' in package 'Matrix'
Creating a generic function for 't' from package 'base' in package 'Matrix'
Creating a generic function for 'diag' from package 'base' in package 'Matrix'
Creating a generic function for 'as.matrix' from package 'base' in package 'Matrix'
Creating a generic function for 'as.array' from package 'base' in package 'Matrix'
Creating a generic function for 'head' from package 'utils' in package 'Matrix'
Creating a generic function for 'tail' from package 'utils' in package 'Matrix'
Creating a generic function for 'drop' from package 'base' in package 'Matrix'
Creating a generic function for 'as.vector' from package 'base' in package 'Matrix'
Creating a generic function for 'mean' from package 'base' in package 'Matrix'
Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix'
Creating a generic function for 'isSymmetric' from package 'base' in package 'Matrix'
Creating a generic function for 'unname' from package 'base' in package 'Matrix'
Creating a generic function for 'chol' from package 'base' in package 'Matrix'
Creating a generic function for 'norm' from package 'base' in package 'Matrix'
Creating a generic function for 'rcond' from 'base' in package 'Matrix'
    (from the saved implicit definition)
Creating a generic function for 'rcond' from package 'base' in package 'Matrix'
Creating a generic function for 'all.equal' from package 'base' in package 'Matrix'
Creating a generic function for 'diff' from package 'base' in package 'Matrix'
in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"dsparseMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csr","dgCMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","dgCMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","CsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"CsparseMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"CsparseMatrix","matrix.coo"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"CsparseMatrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","Matrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","Matrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","Matrix"': no definition for class "matrix.csc"
Creating a generic function for 'colSums' from package 'base' in package 'Matrix'
Creating a generic function for 'colMeans' from package 'base' in package 'Matrix'
Creating a generic function for 'rowSums' from package 'base' in package 'Matrix'
Creating a generic function for 'rowMeans' from package 'base' in package 'Matrix'
in method for 'colSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'rowSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'colMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'rowMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
Creating a generic function for 'zapsmall' from package 'base' in package 'Matrix'
Creating a generic function for 'qr' from package 'base' in package 'Matrix'
Creating a generic function for 'diag<-' from package 'base' in package 'Matrix'
Creating a generic function for 'crossprod' from package 'base' in package 'Matrix'
Creating a generic function for 'tcrossprod' from package 'base' in package 'Matrix'
Creating a generic function for 'print' from package 'base' in package 'Matrix'
Creating a generic function for 'summary' from package 'base' in package 'Matrix'
Creating a generic function for 'which' from package 'base' in package 'Matrix'
in method for 'coerce' with signature '"graphAM","sparseMatrix"': no definition for class "graphAM"
in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph"
in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph"
in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no definition for class "graphNEL"
in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL"
in method for 'coerce' with signature '"sparseMatrix","graph"': no definition for class "graph"
in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL"
in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL"
Creating a generic function for 'format' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.R' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix'
** help
*** installing help indices
** building package indices
Loading required package: Matrix
** installing vignettes
   'Comparisons.Rnw' 
   'Design-issues.Rnw' 
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** testing if installed package can be loaded

* DONE (Matrix)
begin installing recommended package mgcv
* installing *source* package 'mgcv' ...
** libs
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c gdi.c -o gdi.o
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flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c mat.c -o mat.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c matrix.c -o matrix.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c mgcv.c -o mgcv.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c misc.c -o misc.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c qp.c -o qp.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c soap.c -o soap.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c sparse-smooth.c -o sparse-smooth.o
flag-sort -r gcc -ffor-scope -I/sw/build.build/r-base215-2.15.3-112/R-2.15.3/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c tprs.c -o tprs.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o mgcv.dylib gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o qp.o soap.o sparse-smooth.o tprs.o -framework Accelerate -framework Accelerate -L/sw/lib/gcc4.9/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1 -L/sw/lib/gcc4.9/lib -lgfortran -lquadmath -lm /sw/build.build/r-base215-2.15.3-112/R-2.15.3/lib/libR.dylib -lintl -Wl,-framework -Wl,CoreFoundation
installing to /sw/build.build/r-base215-2.15.3-112/R-2.15.3/library/mgcv/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (mgcv)
'pdflatex' is needed to make vignettes but is missing on your system.
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mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/texmf/bibtex/bst
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/texmf/tex
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/texmf/tex/latex
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/bin
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/include
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/include/R_ext
make[3]: Nothing to be done for `install'.
make[3]: Nothing to be done for `install'.
make[3]: Nothing to be done for `install'.
make[3]: Nothing to be done for `install'.
make[3]: Nothing to be done for `install'.
make[3]: Nothing to be done for `install'.
make[3]: Nothing to be done for `install'.
make[3]: Nothing to be done for `install'.
make[2]: Nothing to be done for `install'.
make[2]: Nothing to be done for `install'.
flag-sort -r gcc -ffor-scope -I. -I../../src/include -I../../src/include -I/usr/X11R6/include -I/sw/include -DHAVE_CONFIG_H    -fPIC  -g -O3  -DR_HOME='"/sw/Library/Frameworks/R.framework/Versions/2.15/Resources"' -o Rscript \
	  ./Rscript.c
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/lib
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/lib/pkgconfig
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/bin/exec
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/lib
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/modules
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library
installing packages ...
  building HTML index ...
make[1]: Nothing to be done for `install'.
installing translations:
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/da
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/da/LC_MESSAGES
  da
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/en
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/en/LC_MESSAGES
  en
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/en_GB
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/en_GB/LC_MESSAGES
  en_GB
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/es
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/es/LC_MESSAGES
  es
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/fr
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/fr/LC_MESSAGES
  fr
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/de
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/de/LC_MESSAGES
  de
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/it
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/it/LC_MESSAGES
  it
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/ja
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/ja/LC_MESSAGES
  ja
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/ko
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/ko/LC_MESSAGES
  ko
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/nn
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/nn/LC_MESSAGES
  nn
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/pl
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/pl/LC_MESSAGES
  pl
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/pt_BR
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/pt_BR/LC_MESSAGES
  pt_BR
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/ru
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/ru/LC_MESSAGES
  ru
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/tr
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/tr/LC_MESSAGES
  tr
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/zh_CN
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/zh_CN/LC_MESSAGES
  zh_CN
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/zh_TW
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/zh_TW/LC_MESSAGES
  zh_TW
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/en@quot
mkdir /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/share/locale/en@quot/LC_MESSAGES
  en@quot
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f ./Makefile.fw top_srcdir=. install
Creating R framework ...
  libR
+ cd /sw/build.build/root-r-base215-2.15.3-112/sw
+ perl -pi -e 's|/sw/build.build/root-r-base215-2.15.3-112/sw|/sw|g' Library/Frameworks/R.framework/Resources/bin/R
+ perl -pi -e s,Resources,Versions/2.15/Resources,g Library/Frameworks/R.framework/Resources/bin/R
++ sw_vers -productVersion
+ [[ 10.9.4 > 10.5 ]]
+ perl -pi -e 's|# export PATH|export PATH|' Library/Frameworks/R.framework/Resources/bin/R
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libR.dylib Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libR.dylib
+ pushd Library/Frameworks/R.framework/Resources/
/sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Resources /sw/build.build/root-r-base215-2.15.3-112/sw
+ ln -s /sw/lib/R/2.15/site-library site-library
+ popd
/sw/build.build/root-r-base215-2.15.3-112/sw
+ pushd Library/Frameworks/R.framework/Versions/
/sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions /sw/build.build/root-r-base215-2.15.3-112/sw
+ ln -s 2.15 2.15.3
+ popd
/sw/build.build/root-r-base215-2.15.3-112/sw
+ pushd Library/Frameworks/R.framework/Versions/2.15/Resources/library/
/sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library /sw/build.build/root-r-base215-2.15.3-112/sw
+ LIBS='class cluster foreign grDevices grid KernSmooth lattice MASS Matrix methods mgcv nlme nnet rpart spatial splines stats survival tcltk tools '
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/class/libs/class.dylib class/libs/class.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/cluster/libs/cluster.dylib cluster/libs/cluster.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/foreign/libs/foreign.dylib foreign/libs/foreign.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/grDevices/libs/grDevices.dylib grDevices/libs/grDevices.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/grid/libs/grid.dylib grid/libs/grid.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/KernSmooth/libs/KernSmooth.dylib KernSmooth/libs/KernSmooth.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/lattice/libs/lattice.dylib lattice/libs/lattice.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/MASS/libs/MASS.dylib MASS/libs/MASS.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Matrix/libs/Matrix.dylib Matrix/libs/Matrix.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/methods/libs/methods.dylib methods/libs/methods.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/mgcv/libs/mgcv.dylib mgcv/libs/mgcv.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/nlme/libs/nlme.dylib nlme/libs/nlme.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/nnet/libs/nnet.dylib nnet/libs/nnet.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rpart/libs/rpart.dylib rpart/libs/rpart.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/spatial/libs/spatial.dylib spatial/libs/spatial.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/splines/libs/splines.dylib splines/libs/splines.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/libs/stats.dylib stats/libs/stats.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/survival/libs/survival.dylib survival/libs/survival.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/tcltk/libs/tcltk.dylib tcltk/libs/tcltk.dylib
+ for LIB in '$LIBS'
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/tools/libs/tools.dylib tools/libs/tools.dylib
+ popd
/sw/build.build/root-r-base215-2.15.3-112/sw
+ pushd Library/Frameworks/R.framework/Versions/2.15/Resources/modules
/sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/modules /sw/build.build/root-r-base215-2.15.3-112/sw
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/modules/internet.dylib internet.dylib
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/modules/lapack.dylib lapack.dylib
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/modules/R_X11.dylib R_X11.dylib
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/modules/vfonts.dylib vfonts.dylib
+ popd
/sw/build.build/root-r-base215-2.15.3-112/sw
+ mkdir -p bin
+ pushd bin
/sw/build.build/root-r-base215-2.15.3-112/sw/bin /sw/build.build/root-r-base215-2.15.3-112/sw
+ ln -s /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R R
+ ln -s /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R R-2.15
+ popd
/sw/build.build/root-r-base215-2.15.3-112/sw
+ mkdir -p share/man/man1
+ pushd share/man/man1
/sw/build.build/root-r-base215-2.15.3-112/sw/share/man/man1 /sw/build.build/root-r-base215-2.15.3-112/sw
+ ln -s /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/man1/R.1 R.1
+ popd
/sw/build.build/root-r-base215-2.15.3-112/sw
+ chmod 755 Library/Frameworks/R.framework/Resources/library
+ rm -rf Library/Frameworks/R.framework/Versions/2.15/Resources/library/Matrix/include
+ cd /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/grDevices/libs/cairo.dylib grDevices/libs/cairo.dylib
+ install_name_tool -id /sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library/parallel/libs/parallel.dylib parallel/libs/parallel.dylib
+ perl -pi -e 's|LIBR =|LIBR = -L/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/lib -lR #|' /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/etc/Makeconf
+ chmod -R g-w /sw/build.build/root-r-base215-2.15.3-112/sw
sudo -u fink-bld [ENV] sh -c /tmp/fink.fUVqs
/usr/bin/install -d -m 755 /sw/build.build/root-r-base215-2.15.3-112/sw/etc/profile.d
echo "setenv R_HOME '/sw/Library/Frameworks/R.framework/Versions/2.15/Resources'" >> /sw/build.build/root-r-base215-2.15.3-112/sw/etc/profile.d/r-base215.csh.env
echo "export R_HOME='/sw/Library/Frameworks/R.framework/Versions/2.15/Resources'" >> /sw/build.build/root-r-base215-2.15.3-112/sw/etc/profile.d/r-base215.sh.env
/usr/bin/touch /sw/build.build/root-r-base215-2.15.3-112/sw/etc/profile.d/r-base215.csh
/usr/bin/touch /sw/build.build/root-r-base215-2.15.3-112/sw/etc/profile.d/r-base215.sh
/bin/cat /sw/build.build/root-r-base215-2.15.3-112/sw/etc/profile.d/r-base215.csh >> /sw/build.build/root-r-base215-2.15.3-112/sw/etc/profile.d/r-base215.csh.env
/bin/cat /sw/build.build/root-r-base215-2.15.3-112/sw/etc/profile.d/r-base215.sh >> /sw/build.build/root-r-base215-2.15.3-112/sw/etc/profile.d/r-base215.sh.env
/bin/mv -f /sw/build.build/root-r-base215-2.15.3-112/sw/etc/profile.d/r-base215.csh.env /sw/build.build/root-r-base215-2.15.3-112/sw/etc/profile.d/r-base215.csh
/bin/mv -f /sw/build.build/root-r-base215-2.15.3-112/sw/etc/profile.d/r-base215.sh.env /sw/build.build/root-r-base215-2.15.3-112/sw/etc/profile.d/r-base215.sh
/bin/chmod 755 /sw/build.build/root-r-base215-2.15.3-112/sw/etc/profile.d/r-base215.*
/bin/rm -f /sw/build.build/root-r-base215-2.15.3-112/sw/info/dir /sw/build.build/root-r-base215-2.15.3-112/sw/info/dir.old /sw/build.build/root-r-base215-2.15.3-112/sw/share/info/dir /sw/build.build/root-r-base215-2.15.3-112/sw/share/info/dir.old
/bin/rm -rf /sw/build.build/root-r-base215-shlibs-2.15.3-112
/bin/mkdir -p /sw/build.build/root-r-base215-shlibs-2.15.3-112/sw
/bin/mkdir -p /sw/build.build/root-r-base215-shlibs-2.15.3-112/DEBIAN
/usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-r-base215-shlibs-2.15.3-112
sudo -u fink-bld [ENV] sh -c /tmp/fink.r26M_
/usr/bin/install -d -m 755 /sw/build.build/root-r-base215-shlibs-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources
/bin/mv /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/lib /sw/build.build/root-r-base215-shlibs-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/
/bin/mv /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/library /sw/build.build/root-r-base215-shlibs-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/
/bin/mv /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/modules /sw/build.build/root-r-base215-shlibs-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/
/bin/rm -f /sw/build.build/root-r-base215-shlibs-2.15.3-112/sw/info/dir /sw/build.build/root-r-base215-shlibs-2.15.3-112/sw/info/dir.old /sw/build.build/root-r-base215-shlibs-2.15.3-112/sw/share/info/dir /sw/build.build/root-r-base215-shlibs-2.15.3-112/sw/share/info/dir.old
/bin/rm -rf /sw/build.build/root-r-base215-dev-2.15.3-112
/bin/mkdir -p /sw/build.build/root-r-base215-dev-2.15.3-112/sw
/bin/mkdir -p /sw/build.build/root-r-base215-dev-2.15.3-112/DEBIAN
/usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-r-base215-dev-2.15.3-112
sudo -u fink-bld [ENV] sh -c /tmp/fink.c0sfw
/usr/bin/install -d -m 755 /sw/build.build/root-r-base215-dev-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources
/bin/mv /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/include /sw/build.build/root-r-base215-dev-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/
/usr/bin/install -d -m 755 /sw/build.build/root-r-base215-dev-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15
/bin/mv /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/Headers /sw/build.build/root-r-base215-dev-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/2.15/
/usr/bin/install -d -m 755 /sw/build.build/root-r-base215-dev-2.15.3-112/sw/lib
/bin/mv /sw/build.build/root-r-base215-2.15.3-112/sw/lib/pkgconfig /sw/build.build/root-r-base215-dev-2.15.3-112/sw/lib/
/bin/rm -f /sw/build.build/root-r-base215-dev-2.15.3-112/sw/info/dir /sw/build.build/root-r-base215-dev-2.15.3-112/sw/info/dir.old /sw/build.build/root-r-base215-dev-2.15.3-112/sw/share/info/dir /sw/build.build/root-r-base215-dev-2.15.3-112/sw/share/info/dir.old
/bin/rm -rf /sw/build.build/root-r-base-2.15.3-112
/bin/mkdir -p /sw/build.build/root-r-base-2.15.3-112/sw
/bin/mkdir -p /sw/build.build/root-r-base-2.15.3-112/DEBIAN
/usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-r-base-2.15.3-112
sudo -u fink-bld [ENV] sh -c /tmp/fink.Id0PZ
/usr/bin/install -d -m 755 /sw/build.build/root-r-base-2.15.3-112/sw/Library/Frameworks/R.framework
/bin/mv /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/R /sw/build.build/root-r-base-2.15.3-112/sw/Library/Frameworks/R.framework/
/bin/mv /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Headers /sw/build.build/root-r-base-2.15.3-112/sw/Library/Frameworks/R.framework/
/bin/mv /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Libraries /sw/build.build/root-r-base-2.15.3-112/sw/Library/Frameworks/R.framework/
/bin/mv /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/PrivateHeaders /sw/build.build/root-r-base-2.15.3-112/sw/Library/Frameworks/R.framework/
/bin/mv /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Resources /sw/build.build/root-r-base-2.15.3-112/sw/Library/Frameworks/R.framework/
/usr/bin/install -d -m 755 /sw/build.build/root-r-base-2.15.3-112/sw/Library/Frameworks/R.framework/Versions
/bin/mv /sw/build.build/root-r-base215-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/Current /sw/build.build/root-r-base-2.15.3-112/sw/Library/Frameworks/R.framework/Versions/
/usr/bin/install -d -m 755 /sw/build.build/root-r-base-2.15.3-112/sw/bin
/bin/mv /sw/build.build/root-r-base215-2.15.3-112/sw/bin/R /sw/build.build/root-r-base-2.15.3-112/sw/bin/
/usr/bin/install -d -m 755 /sw/build.build/root-r-base-2.15.3-112/sw
/bin/mv /sw/build.build/root-r-base215-2.15.3-112/sw/share /sw/build.build/root-r-base-2.15.3-112/sw/
/bin/rm -f /sw/build.build/root-r-base-2.15.3-112/sw/info/dir /sw/build.build/root-r-base-2.15.3-112/sw/info/dir.old /sw/build.build/root-r-base-2.15.3-112/sw/share/info/dir /sw/build.build/root-r-base-2.15.3-112/sw/share/info/dir.old
Reverting ownership of install dir to root
Writing control file...
Writing md5sums file...
env LANG=C LC_ALL=C dpkg-deb -b root-r-base215-2.15.3-112 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci
dpkg-deb: building package `r-base215' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/r-base215_2.15.3-112_darwin-x86_64.deb'.
Reverting ownership of install dir to root
Writing control file...
Creating shlibs files...
Writing md5sums file...
env LANG=C LC_ALL=C dpkg-deb -b root-r-base215-shlibs-2.15.3-112 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci
dpkg-deb: building package `r-base215-shlibs' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/r-base215-shlibs_2.15.3-112_darwin-x86_64.deb'.
Reverting ownership of install dir to root
Writing control file...
Writing md5sums file...
env LANG=C LC_ALL=C dpkg-deb -b root-r-base215-dev-2.15.3-112 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci
dpkg-deb: building package `r-base215-dev' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/r-base215-dev_2.15.3-112_darwin-x86_64.deb'.
Reverting ownership of install dir to root
Writing control file...
env LANG=C LC_ALL=C dpkg-deb -b root-r-base-2.15.3-112 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci
dpkg-deb: building package `r-base' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/r-base_2.15.3-112_darwin-x86_64.deb'.
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-r-base215-2.15.3-112
(Reading database ... 14409 files and directories currently installed.)
Removing fink-buildlock-r-base215-2.15.3-112 ...