01.autoconf

2015-08-08 18:31:58 +1000

autoconf

02.configure

2015-08-08 18:31:58 +1000

./configure
--prefix=/bio/linuxbrew/Cellar/harvest-tools/1.2
--with-protobuf=/bio/linuxbrew/opt/protobuf
--with-capnp=/bio/linuxbrew/opt/capnp

checking for protoc... yes
checking for capnp... yes
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 /bio/linuxbrew/bin/g++-5 accepts -g... yes
checking how to run the C++ preprocessor... /bio/linuxbrew/bin/g++-5 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
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 google/protobuf/stubs/common.h usability... yes
checking google/protobuf/stubs/common.h presence... yes
checking for google/protobuf/stubs/common.h... yes
checking capnp/common.h usability... yes
checking capnp/common.h presence... yes
checking for capnp/common.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
configure: creating ./config.status
config.status: creating Makefile

03.make

2015-08-08 18:31:59 +1000

make
all

cd src; /bio/linuxbrew/opt/protobuf/bin/protoc --cpp_out . harvest/pb/harvest.proto
cd src/harvest/capnp;/bio/linuxbrew/opt/capnp/bin/capnp compile -oc++ harvest.capnp
cd src; /bio/linuxbrew/opt/protobuf/bin/protoc --cpp_out . harvest/pb/harvest.proto
cd src/harvest/capnp;/bio/linuxbrew/opt/capnp/bin/capnp compile -oc++ harvest.capnp
/bio/linuxbrew/bin/gcc-5 -c -o src/harvest/memcpyWrap.o src/harvest/memcpyWrap.c
harvest.capnp:9:20-38: error: Import failed: /capnp/c++.capnp
harvest.capnp:10:2-5: error: Not defined: Cxx
make: *** [src/harvest/capnp/harvest.capnp.h] Error 1
make: *** Waiting for unfinished jobs....
harvest.capnp:9:20-38: error: Import failed: /capnp/c++.capnp
harvest.capnp:10:2-5: error: Not defined: Cxx
make: *** [src/harvest/capnp/harvest.capnp.c++] Error 1

HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/linuxbrew
HEAD: 519dc5ffa1c01efa1be30676388fd1a8166caf4a
Last commit: 32 hours ago
HOMEBREW_PREFIX: /bio/linuxbrew
HOMEBREW_CELLAR: /bio/linuxbrew/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com
CPU: 72-core 64-bit 6
OS X: 0-x86_64
Xcode: N/A
CLT: N/A
Clang: N/A
X11: N/A
System Ruby: 2.2.2 => /bio/linuxbrew/Cellar/ruby/2.2.2/bin/ruby
Perl: /usr/bin/perl
Python: /bio/linuxbrew/bin/python => /bio/linuxbrew/Cellar/python/2.7.10/bin/python2.7
Ruby: /bio/linuxbrew/bin/ruby => /bio/linuxbrew/Cellar/ruby/2.2.2/bin/ruby
Java: 1.7.0_85

CC: /bio/linuxbrew/bin/gcc-5 => /bio/linuxbrew/Cellar/gcc/5.2.0/bin/gcc-5
CXX: /bio/linuxbrew/bin/g++-5 => /bio/linuxbrew/Cellar/gcc/5.2.0/bin/g++-5
OBJC: /bio/linuxbrew/bin/gcc-5
OBJCXX: /bio/linuxbrew/bin/g++-5
CFLAGS: -Os -w -pipe -march=core2
CXXFLAGS: -Os -w -pipe -march=core2
CPPFLAGS: -isystem/bio/linuxbrew/include
LDFLAGS: -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib
MAKEFLAGS: -j72
CMAKE_PREFIX_PATH: /bio/linuxbrew
PKG_CONFIG_LIBDIR: /bio/linuxbrew/lib/pkgconfig
PATH: /bio/linuxbrew/bin:/home/tseemann/perl5/bin:/bio/perl5/bin:/bio/linuxbrew/bin:/bio/linuxbrew/sbin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bio/sw/hierBAPS:/bio/sw/brat:/bio/sw/mauve:/bio/sw/splitstree4:/bio/sw/vbc/fqa-tools:/bio/sw/vbc/misc:/bio/sw/MUMmer:/bio/sw/tablet:/bio/sw/nesoni/bin:/home/tseemann/git/wombac/bin:/home/tseemann/git/snippy/bin:/home/tseemann/git/barrnap/bin:/home/tseemann/git/nullarbor/bin:/home/tseemann/git/prokka/bin:/home/tseemann/git/mlst/bin:/home/tseemann/git/abricate/bin:/home/tseemann/git/mdu-tools/bin:/usr/local/sbin:/usr/sbin:/home/tseemann/.local/bin:/home/tseemann/bin:/bio/linuxbrew/Library/ENV/scm

config.log

This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by configure, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  $ ./configure --prefix=/bio/linuxbrew/Cellar/harvest-tools/1.2 --with-protobuf=/bio/linuxbrew/opt/protobuf --with-capnp=/bio/linuxbrew/opt/capnp

## --------- ##
## Platform. ##
## --------- ##

hostname = 526080-s598783.unimelb.edu.au
uname -m = x86_64
uname -r = 3.10.0-229.4.2.el7.x86_64
uname -s = Linux
uname -v = #1 SMP Fri Apr 24 15:26:38 EDT 2015

/usr/bin/uname -p = x86_64
/bin/uname -X     = unknown

/bin/arch              = x86_64
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo      = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /bio/linuxbrew/bin
PATH: /home/tseemann/perl5/bin
PATH: /bio/perl5/bin
PATH: /bio/linuxbrew/bin
PATH: /bio/linuxbrew/sbin
PATH: /usr/lib64/qt-3.3/bin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bio/sw/hierBAPS
PATH: /bio/sw/brat
PATH: /bio/sw/mauve
PATH: /bio/sw/splitstree4
PATH: /bio/sw/vbc/fqa-tools
PATH: /bio/sw/vbc/misc
PATH: /bio/sw/MUMmer
PATH: /bio/sw/tablet
PATH: /bio/sw/nesoni/bin
PATH: /home/tseemann/git/wombac/bin
PATH: /home/tseemann/git/snippy/bin
PATH: /home/tseemann/git/barrnap/bin
PATH: /home/tseemann/git/nullarbor/bin
PATH: /home/tseemann/git/prokka/bin
PATH: /home/tseemann/git/mlst/bin
PATH: /home/tseemann/git/abricate/bin
PATH: /home/tseemann/git/mdu-tools/bin
PATH: /usr/local/sbin
PATH: /usr/sbin
PATH: /home/tseemann/.local/bin
PATH: /home/tseemann/bin
PATH: /bio/linuxbrew/Library/ENV/scm


## ----------- ##
## Core tests. ##
## ----------- ##

configure:2010: checking for protoc
configure:2026: found /bio/linuxbrew/opt/protobuf/bin/protoc
configure:2038: result: yes
configure:2054: checking for capnp
configure:2070: found /bio/linuxbrew/opt/capnp/bin/capnp
configure:2082: result: yes
configure:2210: checking for C++ compiler version
configure:2219: /bio/linuxbrew/bin/g++-5 --version >&5
g++-5 (Homebrew gcc 5.2.0) 5.2.0
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:2230: $? = 0
configure:2219: /bio/linuxbrew/bin/g++-5 -v >&5
Reading specs from /bio/linuxbrew/Cellar/gcc/5.2.0/lib/gcc/x86_64-unknown-linux-gnu/5.2.0/specs
COLLECT_GCC=/bio/linuxbrew/bin/g++-5
COLLECT_LTO_WRAPPER=/bio/linuxbrew/Cellar/gcc/5.2.0/libexec/gcc/x86_64-unknown-linux-gnu/5.2.0/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../configure --prefix=/bio/linuxbrew/Cellar/gcc/5.2.0  --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-5 --with-gmp=/bio/linuxbrew/opt/gmp --with-mpfr=/bio/linuxbrew/opt/mpfr --with-mpc=/bio/linuxbrew/opt/libmpc --with-isl=/bio/linuxbrew/opt/isl --with-system-zlib --enable-libstdcxx-time=yes --enable-stage1-checking --enable-checking=release --enable-lto --with-build-config=bootstrap-debug --disable-werror --with-pkgversion='Homebrew gcc 5.2.0' --with-bugurl=https://github.com/Homebrew/homebrew/issues --enable-plugin --disable-nls --disable-multilib
Thread model: posix
gcc version 5.2.0 (Homebrew gcc 5.2.0) 
configure:2230: $? = 0
configure:2219: /bio/linuxbrew/bin/g++-5 -V >&5
g++-5: error: unrecognized command line option '-V'
g++-5: fatal error: no input files
compilation terminated.
configure:2230: $? = 1
configure:2219: /bio/linuxbrew/bin/g++-5 -qversion >&5
g++-5: error: unrecognized command line option '-qversion'
g++-5: fatal error: no input files
compilation terminated.
configure:2230: $? = 1
configure:2250: checking whether the C++ compiler works
configure:2272: /bio/linuxbrew/bin/g++-5 -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.cpp  >&5
configure:2276: $? = 0
configure:2324: result: yes
configure:2327: checking for C++ compiler default output file name
configure:2329: result: a.out
configure:2335: checking for suffix of executables
configure:2342: /bio/linuxbrew/bin/g++-5 -o conftest -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.cpp  >&5
configure:2346: $? = 0
configure:2368: result: 
configure:2390: checking whether we are cross compiling
configure:2398: /bio/linuxbrew/bin/g++-5 -o conftest -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.cpp  >&5
configure:2402: $? = 0
configure:2409: ./conftest
configure:2413: $? = 0
configure:2428: result: no
configure:2433: checking for suffix of object files
configure:2455: /bio/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp >&5
configure:2459: $? = 0
configure:2480: result: o
configure:2484: checking whether we are using the GNU C++ compiler
configure:2503: /bio/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp >&5
configure:2503: $? = 0
configure:2512: result: yes
configure:2521: checking whether /bio/linuxbrew/bin/g++-5 accepts -g
configure:2541: /bio/linuxbrew/bin/g++-5 -c -g -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp >&5
configure:2541: $? = 0
configure:2582: result: yes
configure:2611: checking how to run the C++ preprocessor
configure:2638: /bio/linuxbrew/bin/g++-5 -E -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp
configure:2638: $? = 0
configure:2652: /bio/linuxbrew/bin/g++-5 -E -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp
conftest.cpp:9:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:2652: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:2677: result: /bio/linuxbrew/bin/g++-5 -E
configure:2697: /bio/linuxbrew/bin/g++-5 -E -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp
configure:2697: $? = 0
configure:2711: /bio/linuxbrew/bin/g++-5 -E -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp
conftest.cpp:9:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:2711: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:2740: checking for grep that handles long lines and -e
configure:2798: result: /usr/bin/grep
configure:2803: checking for egrep
configure:2865: result: /usr/bin/grep -E
configure:2870: checking for ANSI C header files
configure:2890: /bio/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp >&5
configure:2890: $? = 0
configure:2963: /bio/linuxbrew/bin/g++-5 -o conftest -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib conftest.cpp  >&5
configure:2963: $? = 0
configure:2963: ./conftest
configure:2963: $? = 0
configure:2974: result: yes
configure:2987: checking for sys/types.h
configure:2987: /bio/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp >&5
configure:2987: $? = 0
configure:2987: result: yes
configure:2987: checking for sys/stat.h
configure:2987: /bio/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp >&5
configure:2987: $? = 0
configure:2987: result: yes
configure:2987: checking for stdlib.h
configure:2987: /bio/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp >&5
configure:2987: $? = 0
configure:2987: result: yes
configure:2987: checking for string.h
configure:2987: /bio/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp >&5
configure:2987: $? = 0
configure:2987: result: yes
configure:2987: checking for memory.h
configure:2987: /bio/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp >&5
configure:2987: $? = 0
configure:2987: result: yes
configure:2987: checking for strings.h
configure:2987: /bio/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp >&5
configure:2987: $? = 0
configure:2987: result: yes
configure:2987: checking for inttypes.h
configure:2987: /bio/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp >&5
configure:2987: $? = 0
configure:2987: result: yes
configure:2987: checking for stdint.h
configure:2987: /bio/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp >&5
configure:2987: $? = 0
configure:2987: result: yes
configure:2987: checking for unistd.h
configure:2987: /bio/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp >&5
configure:2987: $? = 0
configure:2987: result: yes
configure:2999: checking google/protobuf/stubs/common.h usability
configure:2999: /bio/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp >&5
configure:2999: $? = 0
configure:2999: result: yes
configure:2999: checking google/protobuf/stubs/common.h presence
configure:2999: /bio/linuxbrew/bin/g++-5 -E -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp
configure:2999: $? = 0
configure:2999: result: yes
configure:2999: checking for google/protobuf/stubs/common.h
configure:2999: result: yes
configure:3013: checking capnp/common.h usability
configure:3013: /bio/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp >&5
configure:3013: $? = 0
configure:3013: result: yes
configure:3013: checking capnp/common.h presence
configure:3013: /bio/linuxbrew/bin/g++-5 -E -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp
configure:3013: $? = 0
configure:3013: result: yes
configure:3013: checking for capnp/common.h
configure:3013: result: yes
configure:3027: checking zlib.h usability
configure:3027: /bio/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=core2 -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp >&5
configure:3027: $? = 0
configure:3027: result: yes
configure:3027: checking zlib.h presence
configure:3027: /bio/linuxbrew/bin/g++-5 -E -I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11 conftest.cpp
configure:3027: $? = 0
configure:3027: result: yes
configure:3027: checking for zlib.h
configure:3027: result: yes
configure:3198: creating ./config.status

## ---------------------- ##
## Running config.status. ##
## ---------------------- ##

This file was extended by config.status, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  CONFIG_FILES    = 
  CONFIG_HEADERS  = 
  CONFIG_LINKS    = 
  CONFIG_COMMANDS = 
  $ ./config.status 

on 526080-s598783.unimelb.edu.au

config.status:727: creating Makefile

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CPPFLAGS_set=set
ac_cv_env_CPPFLAGS_value=-isystem/bio/linuxbrew/include
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=set
ac_cv_env_CXXFLAGS_value='-Os -w -pipe -march=core2'
ac_cv_env_CXX_set=set
ac_cv_env_CXX_value=/bio/linuxbrew/bin/g++-5
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value='-L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib'
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_header_capnp_common_h=yes
ac_cv_header_google_protobuf_stubs_common_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_header_zlib_h=yes
ac_cv_objext=o
ac_cv_path_EGREP='/usr/bin/grep -E'
ac_cv_path_GREP=/usr/bin/grep
ac_cv_prog_CXXCPP='/bio/linuxbrew/bin/g++-5 -E'
ac_cv_prog_capnpCheck=yes
ac_cv_prog_cxx_g=yes
ac_cv_prog_protocCheck=yes

## ----------------- ##
## Output variables. ##
## ----------------- ##

CPPFLAGS='-I/bio/linuxbrew/opt/protobuf/include -I/bio/linuxbrew/opt/capnp/include -std=c++11'
CXX='/bio/linuxbrew/bin/g++-5'
CXXCPP='/bio/linuxbrew/bin/g++-5 -E'
CXXFLAGS='-Os -w -pipe -march=core2'
DEFS='-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/usr/bin/grep -E'
EXEEXT=''
GREP='/usr/bin/grep'
LDFLAGS='-L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib'
LIBOBJS=''
LIBS=''
LTLIBOBJS=''
OBJEXT='o'
PACKAGE_BUGREPORT=''
PACKAGE_NAME=''
PACKAGE_STRING=''
PACKAGE_TARNAME=''
PACKAGE_URL=''
PACKAGE_VERSION=''
PATH_SEPARATOR=':'
SHELL='/bin/sh'
ac_ct_CXX=''
bindir='${exec_prefix}/bin'
build_alias=''
capnp='/bio/linuxbrew/opt/capnp'
capnpCheck='yes'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host_alias=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/bio/linuxbrew/Cellar/harvest-tools/1.2'
program_transform_name='s,x,x,'
protobuf='/bio/linuxbrew/opt/protobuf'
protocCheck='yes'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

/* confdefs.h */
#define PACKAGE_NAME ""
#define PACKAGE_TARNAME ""
#define PACKAGE_VERSION ""
#define PACKAGE_STRING ""
#define PACKAGE_BUGREPORT ""
#define PACKAGE_URL ""
#define STDC_HEADERS 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1

configure: exit 0

config.out

HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/linuxbrew
HEAD: 519dc5ffa1c01efa1be30676388fd1a8166caf4a
Last commit: 32 hours ago
HOMEBREW_PREFIX: /bio/linuxbrew
HOMEBREW_CELLAR: /bio/linuxbrew/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com
CPU: 72-core 64-bit 6
OS X: 0-x86_64
Xcode: N/A
CLT: N/A
Clang: N/A
X11: N/A
System Ruby: 2.2.2 => /bio/linuxbrew/Cellar/ruby/2.2.2/bin/ruby
Perl: /usr/bin/perl
Python: /bio/linuxbrew/bin/python => /bio/linuxbrew/Cellar/python/2.7.10/bin/python2.7
Ruby: /bio/linuxbrew/bin/ruby => /bio/linuxbrew/Cellar/ruby/2.2.2/bin/ruby
Java: 1.7.0_85

doctor.out

Your system is ready to brew.

tap.out

Formula: harvest-tools
Tap: homebrew/homebrew-science
Path: /bio/linuxbrew/Library/Taps/homebrew/homebrew-science/harvest-tools.rb