Removing old build environment
BUILD START: r-base-3.3.0-0
Fetching package metadata .........
Solving package specifications: ..........
gcc install OS matches gcc build OS: Skipping post-link portability fixes.
prepending /home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/bin to PATH
patching file src/extra/trio/Makefile.win
patching file src/gnuwin32/fixed/etc/Makeconf
patching file src/gnuwin32/fixed/etc/Makeconf
Hunk #1 succeeded at 58 (offset 1 line).
patching file src/main/eval.c
Hunk #1 succeeded at 3753 (offset 130 lines).
patching file src/main/eval.c
Hunk #1 succeeded at 3754 (offset 130 lines).
patching file src/main/main.c
Hunk #1 succeeded at 770 (offset 28 lines).
patching file configure.ac
patching file configure
+ export CFLAGS=-I/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/include
+ CFLAGS=-I/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/include
+ export CPPFLAGS=-I/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/include
+ CPPFLAGS=-I/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/include
+ export 'FFLAGS=-I/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/include -L/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib'
+ FFLAGS='-I/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/include -L/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib'
+ export 'FCFLAGS=-I/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/include -L/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib'
+ FCFLAGS='-I/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/include -L/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib'
+ export OBJCFLAGS=-I/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/include
+ OBJCFLAGS=-I/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/include
+ export CXXFLAGS=-I/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/include
+ CXXFLAGS=-I/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/include
+ export 'LDFLAGS= -L/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib -lgfortran'
+ LDFLAGS=' -L/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib -lgfortran'
+ export 'LAPACK_LDFLAGS=-L/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib -lgfortran'
+ LAPACK_LDFLAGS='-L/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib -lgfortran'
+ export PKG_CPPFLAGS=-I/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/include
+ PKG_CPPFLAGS=-I/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/include
+ export 'PKG_LDFLAGS=-L/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib -lgfortran'
+ PKG_LDFLAGS='-L/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib -lgfortran'
+ export TCL_CONFIG=/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib/tclConfig.sh
+ TCL_CONFIG=/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib/tclConfig.sh
+ export TK_CONFIG=/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib/tkConfig.sh
+ TK_CONFIG=/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib/tkConfig.sh
+ export TCL_LIBRARY=/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib/tcl8.5
+ TCL_LIBRARY=/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib/tcl8.5
+ export TK_LIBRARY=/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib/tk8.5
+ TK_LIBRARY=/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib/tk8.5
+ case `uname` in
++ uname
+ Linux
+ . /media/sf_conda/conda-recipes/r-base/java.rc
++ export JDK_HOME=/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.45.x86_64
++ JDK_HOME=/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.45.x86_64
++ export JAVA_HOME=/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.45.x86_64/jre
++ JAVA_HOME=/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.45.x86_64/jre
+ '[' -n /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.45.x86_64 -a -n /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.45.x86_64/jre ']'
+ export 'JAVA_CPPFLAGS=-I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.45.x86_64/include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.45.x86_64/include/linux'
+ JAVA_CPPFLAGS='-I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.45.x86_64/include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.45.x86_64/include/linux'
+ export JAVA_LD_LIBRARY_PATH=/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.45.x86_64/jre/lib/amd64/server
+ JAVA_LD_LIBRARY_PATH=/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.45.x86_64/jre/lib/amd64/server
+ mkdir -p /home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib
+ ./configure --prefix=/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho --enable-shared --enable-R-shlib --enable-BLAS-shlib --disable-R-profiling --disable-prebuilt-html --disable-memory-profiling --with-tk-config=/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib/tkConfig.sh --with-tcl-config=/home/ray/mc-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_placeho/lib/tclConfig.sh --with-x --with-pic --with-cairo --with-recommended-packages=no LIBnn=lib
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking for working aclocal... missing
checking for working autoconf... missing
checking for working automake... missing
checking for working autoheader... missing
checking whether ln -s works... yes
checking for bison... no
checking for byacc... no
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /bin/sed
checking for which... /usr/bin/which
checking for less... /usr/bin/less
checking for gtar... /bin/gtar
checking for tex... no
checking for pdftex... no
configure: WARNING: you cannot build PDF versions of the R manuals
checking for pdflatex... no
configure: WARNING: you cannot build PDF versions of vignettes and help pages
checking for makeindex... no
checking for texi2any... no
configure: WARNING: you cannot build info or HTML versions of the R manuals
checking for texi2dvi... no
checking for kpsewhich... no
checking for latex inconsolata package... checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /usr/bin/gzip
checking for bzip2... /usr/bin/bzip2
checking for firefox... /usr/bin/firefox
using default browser ... /usr/bin/firefox
checking for acroread... no
checking for acroread4... no
checking for xdg-open... no
checking for evince... /usr/bin/evince
checking for notangle... false
checking for realpath... false
checking for pkg-config... /usr/bin/pkg-config
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether gcc needs -traditional... no
checking how to run the C preprocessor... gcc -E
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether __attribute__((visibility())) is supported... yes
checking whether gcc accepts -fvisibility... yes
checking whether gfortran accepts -fvisibility... yes
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking 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 g++ can compile ObjC++... no
no working ObjC++ compiler found
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 98304
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking for gawk... gawk
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
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 how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... yes
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
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... no
checking for main in -lncurses... no
checking for main in -ltermcap... no
checking for main in -ltermlib... no
checking for rl_callback_read_char in -lreadline... no
checking for history_truncate_file... no
configure: error: --with-readline=yes (default) and headers/libs are not available

The following NEW packages will be INSTALLED:

    bzip2:      1.0.6-3   defaults
    cairo:      1.12.18-6 defaults
    cloog:      0.18.0-0  defaults
    curl:       7.49.0-0  defaults
    fontconfig: 2.11.1-5  defaults
    freetype:   2.5.5-1   defaults
    gcc:        4.8.5-6   local   
    glib:       2.43.0-0  defaults
    gmp:        5.1.2-2   defaults
    gsl:        2.1-1     local   
    harfbuzz:   0.9.39-0  defaults
    isl:        0.12.2-0  defaults
    jbig:       2.1-0     defaults
    jpeg:       8d-0      defaults
    libffi:     3.2.1-0   defaults
    libgcc:     5.2.0-0   defaults
    libpng:     1.6.17-0  defaults
    libtiff:    4.0.6-2   defaults
    libxml2:    2.9.2-0   defaults
    mpc:        1.0.1-0   defaults
    mpfr:       3.1.2-0   defaults
    ncurses:    5.9-0     defaults
    openssl:    1.0.2h-1  defaults
    pango:      1.39.0-0  defaults
    pcre:       8.39-0    local   
    pixman:     0.32.6-0  defaults
    readline:   6.2-2     defaults
    tk:         8.5.18-0  defaults
    xz:         5.2.2-0   defaults
    zlib:       1.2.8-3   defaults

Linking packages ...
[                    ]|                                                  |   0%
[bzip2               ]|                                                  |   0%
[gmp                 ]|#                                                 |   3%
[jbig                ]|###                                               |   6%
[jpeg                ]|#####                                             |  10%
[libffi              ]|######                                            |  13%
[libgcc              ]|########                                          |  16%
[libpng              ]|##########                                        |  20%
[ncurses             ]|###########                                       |  23%
[openssl             ]|#############                                     |  26%
[pcre                ]|###############                                   |  30%
[pixman              ]|################                                  |  33%
[readline            ]|##################                                |  36%
[tk                  ]|####################                              |  40%
[xz                  ]|#####################                             |  43%
[zlib                ]|#######################                           |  46%
[curl                ]|#########################                         |  50%
[freetype            ]|##########################                        |  53%
[glib                ]|############################                      |  56%
[gsl                 ]|##############################                    |  60%
[isl                 ]|###############################                   |  63%
[libtiff             ]|#################################                 |  66%
[libxml2             ]|###################################               |  70%
[mpfr                ]|####################################              |  73%
[cloog               ]|######################################            |  76%
[fontconfig          ]|########################################          |  80%
[mpc                 ]|#########################################         |  83%
[cairo               ]|###########################################       |  86%
[gcc                 ]|#############################################     |  90%
[harfbuzz            ]|##############################################    |  93%
[pango               ]|################################################  |  96%
[      COMPLETE      ]|##################################################| 100%
Source cache directory is: /home/ray/mc-x64-3.5/conda-bld/src_cache
Found source in cache: R-3.3.0.tar.gz
Extracting download
Applying patch: '/media/sf_conda/conda-recipes/r-base/0002-Win32-Fix-trio-config-h-include-depth-issue.patch'
Applying patch: '/media/sf_conda/conda-recipes/r-base/0003-Win32-Do-not-static-libgcc-link.patch'
Applying patch: '/media/sf_conda/conda-recipes/r-base/0004-Win32-Use-TCL_VERSION_86.patch'
Applying patch: '/media/sf_conda/conda-recipes/r-base/0005-Win32-Extend-sqrt-NA_real_-hack-to-all-GCC-versions.patch'
Applying patch: '/media/sf_conda/conda-recipes/r-base/0006-Win32-GCC-5.3-Fix-ISNAN-int-emits-UD2-insn.patch'
Applying patch: '/media/sf_conda/conda-recipes/r-base/0007-Win32-MSYS2-ENV_CONV_EXCL_R_ARCH.patch'
Applying patch: '/media/sf_conda/conda-recipes/r-base/0008-Darwin-set-DYLD_FALLBACK_LIBRARY_PATH.patch'
Package: r-base-3.3.0-0
source tree in: /home/ray/mc-x64-3.5/conda-bld/work/R-3.3.0
Command failed: /bin/bash -x -e /media/sf_conda/conda-recipes/r-base/build.sh
