I'm attempting to install cufflinks 2.0.1 on my Windows 7 system using Cygwin. I have done all of the installation steps up to the Make command, but that make command keeps on failing for some reason. I was wondering if anyone could tell me why. I'm using Boost version 1.50
First, here's what happens when I run the configure file:
Benjamin S#BenjaminS-HP /cygdrive/c/analysistools/cufflinks-2.0.1
$ ./configure --prefix=/cygdrive/c/analysistools/cufflinks --with-boost=/cygdrive/c/AnalysisTools/boost --with-bam=/cygdrive/c/analysistools/samtools/samtools
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gawk... (cached) gawk
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.exe
checking for suffix of executables... .exe
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 g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
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 dependency style of gcc... gcc3
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking for a Python interpreter with version >= 2.4... python
checking for python... /usr/bin/python
checking for python version... 2.6
checking for python platform... cygwin
checking for python script directory... ${prefix}/lib/python2.6/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.6/site-packages
checking for boostlib >= 1.47.0... yes
checking for bamlib... yes
checking build system type... i686-pc-cygwin
checking whether the Boost::Thread library is available... yes
checking for exit in -lboost_thread... yes
checking how to run the C preprocessor... gcc -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 if zlib is wanted... yes
checking for inflateEnd in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for inflateEnd in -lz... (cached) yes
checking zlib in /usr... ok
checking for eigenlib... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for pid_t... yes
checking for size_t... yes
checking for ptrdiff_t... yes
checking host system type... i686-pc-cygwin
checking if gcc accepts -m64... no
checking for struct sysinfo.totalram... yes
checking whether sysctl is declared... no
checking whether CTL_HW is declared... no
checking whether HW_PHYSMEM is declared... no
checking how to create a pax tar archive... gnutar
checking dependency style of gcc... (cached) gcc3
checking dependency style of g++... (cached) gcc3
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
-- cufflinks 2.0.1 Configuration Results --
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -pthread -I/cygdrive/c/AnalysisTools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include
GCC version: gcc (GCC) 4.5.3
Host System type: i686-pc-cygwin
Install prefix: /cygdrive/c/analysistools/cufflinks
Install eprefix: ${prefix}
See config.h for further configuration information.
Then here is what happens when I try to make it:
Benjamin S#BenjaminS-HP /cygdrive/c/analysistools/cufflinks-2.0.1
$ make
make all-recursive
make[1]: Entering directory `/cygdrive/c/analysistools/cufflinks-2.0.1'
Making all in src
make[2]: Entering directory `/cygdrive/c/analysistools/cufflinks-2.0.1/src'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -pthread -I/cygdrive/c/AnalysisTools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT clustering.o -MD -MP -MF .deps/clustering.Tpo -c -o clustering.o clustering.cpp
g++: unrecognized option '-pthread'
mv -f .deps/clustering.Tpo .deps/clustering.Po
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -pthread -I/cygdrive/c/AnalysisTools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT differential.o -MD -MP -MF .deps/differential.Tpo -c -o differential.o differential.cpp
g++: unrecognized option '-pthread'
In file included from differential.h:29:0,
from differential.cpp:18:
replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&)’:
replicates.h:152:50: warning: unused variable ‘s2’
In file included from differential.cpp:18:0:
differential.h: In constructor ‘FPKMContext::FPKMContext(double, double, double, double, const CountPerReplicateTable&, double, const FPKMPerReplicateTable&, double, AbundanceStatus, const StatusPerReplicateTable&)’:
differential.h:142:21: warning: ‘FPKMContext::status’ will be initialized after
differential.h:139:29: warning: ‘StatusPerReplicateTable FPKMContext::status_per_rep’
differential.h:131:2: warning: when initialized here
differential.cpp: In member function ‘void TestLauncher::perform_testing(std::vector<boost::shared_ptr<SampleAbundances> >&)’:
differential.cpp:212:31: warning: unused variable ‘s2’
differential.cpp: In member function ‘void TestLauncher::record_tracking_data(std::vector<boost::shared_ptr<SampleAbundances> >&)’:
differential.cpp:240:31: warning: unused variable ‘s2’
differential.cpp: In function ‘SampleDifference get_ds_tests(const AbundanceGroup&, const AbundanceGroup&, bool)’:
differential.cpp:790:16: warning: unused variable ‘name’
differential.cpp: In function ‘void test_differential(const std::string&, const std::vector<boost::shared_ptr<SampleAbundances> >&, Tests&, Tracking&, bool)’:
differential.cpp:1771:83: warning: comparison between signed and unsigned integer expressions
differential.cpp:1772:83: warning: comparison between signed and unsigned integer expressions
differential.cpp:1814:83: warning: comparison between signed and unsigned integer expressions
differential.cpp:1815:83: warning: comparison between signed and unsigned integer expressions
differential.cpp:1856:83: warning: comparison between signed and unsigned integer expressions
differential.cpp:1857:83: warning: comparison between signed and unsigned integer expressions
mv -f .deps/differential.Tpo .deps/differential.Po
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -pthread -I/cygdrive/c/AnalysisTools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT common.o -MD -MP -MF .deps/common.Tpo -c -o common.o common.cpp
g++: unrecognized option '-pthread'
In file included from common.cpp:28:0:
replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&)’:
replicates.h:152:50: warning: unused variable ‘s2’
mv -f .deps/common.Tpo .deps/common.Po
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -pthread -I/cygdrive/c/AnalysisTools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT assemble.o -MD -MP -MF .deps/assemble.Tpo -c -o assemble.o assemble.cpp
g++: unrecognized option '-pthread'
mv -f .deps/assemble.Tpo .deps/assemble.Po
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -pthread -I/cygdrive/c/AnalysisTools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT tokenize.o -MD -MP -MF .deps/tokenize.Tpo -c -o tokenize.o tokenize.cpp
g++: unrecognized option '-pthread'
mv -f .deps/tokenize.Tpo .deps/tokenize.Po
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -pthread -I/cygdrive/c/AnalysisTools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT abundances.o -MD -MP -MF .deps/abundances.Tpo -c -o abundances.o abundances.cpp
g++: unrecognized option '-pthread'
In file included from abundances.cpp:35:0:
replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&)’:
replicates.h:152:50: warning: unused variable ‘s2’
abundances.cpp: In function ‘void collapse_equivalent_hits(const std::vector<MateHit>&, std::vector<boost::shared_ptr<Abundance> >&, std::vector<boost::shared_ptr<Abundance> >&, std::vector<MateHit>&, std::vector<double>&, bool)’:
abundances.cpp:769:28: warning: comparison between signed and unsigned integer expressions
abundances.cpp: In function ‘long double solve_beta(long double, long double, long double)’:
abundances.cpp:1227:145: error: ‘sqrtl’ was not declared in this scope
abundances.cpp: In member function ‘void AbundanceGroup::calculate_FPKM_covariance()’:
abundances.cpp:1780:24: warning: unused variable ‘fpkm’
abundances.cpp: In function ‘void calculate_assignment_probs(const Eigen::VectorXd&, const Eigen::MatrixXd&, const Eigen::VectorXd&, Eigen::MatrixXd&)’:
abundances.cpp:2205:58: warning: comparison between signed and unsigned integer expressions
abundances.cpp: In function ‘AbundanceStatus gamma_mle(const std::vector<boost::shared_ptr<Abundance> >&, const std::vector<MateHit>&, const std::vector<double>&, std::vector<double>&, bool)’:
abundances.cpp:3300:48: warning: comparison between signed and unsigned integer expressions
abundances.cpp:3302:52: warning: comparison between signed and unsigned integer expressions
In file included from abundances.cpp:36:0:
sampling.h: In function ‘double boost::numeric::ublas::cholesky_factorize(M&) [with M = boost::numeric::ublas::matrix<double>]’:
abundances.cpp:117:45: instantiated from here
sampling.h:83:7: error: ‘sqrtl’ was not declared in this scope
/cygdrive/c/AnalysisTools/boost/include/boost/system/error_code.hpp: At global scope:
/cygdrive/c/AnalysisTools/boost/include/boost/system/error_code.hpp:214:36: warning: ‘boost::system::posix_category’ defined but not used
/cygdrive/c/AnalysisTools/boost/include/boost/system/error_code.hpp:215:36: warning: ‘boost::system::errno_ecat’ defined but not used
/cygdrive/c/AnalysisTools/boost/include/boost/system/error_code.hpp:216:36: warning: ‘boost::system::native_ecat’ defined but not used
Makefile:1444: recipe for target `abundances.o' failed
make[2]: *** [abundances.o] Error 1
make[2]: Leaving directory `/cygdrive/c/analysistools/cufflinks-2.0.1/src'
Makefile:290: recipe for target `all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/cygdrive/c/analysistools/cufflinks-2.0.1'
Makefile:228: recipe for target `all' failed
make: *** [all] Error 2
I'm still a bit of an amateur when it comes to cygwin and several bioinformatics programs that require it for me, so I appreciate whatever help you can give.
It looks like you are missing the sqrtl function:
abundances.cpp:1227:145: error: ‘sqrtl’ was not declared in this scope
I do see this defined in Cygwin 1.7.16 in math.h as:
extern long double sqrtl _PARAMS((long double));
Are you running 1.7.16 of Cygwin? Check your /usr/include/math.h and see if sqrtl is defined.
However, I'd be careful running this in Cygwin. Officially cygwin says sqrtl isn't implemented, but I can build a test program to use it. I'm not seeing the results I'd expect, although my C is a bit rusty.
Related
I'm running Octave 4.0.3 on OSX 10.10.5. When I try to install the instrument-control package using:
>> pkg install -forge instrument-control -verbose
I get the following error:
clang: warning: argument unused during compilation: '-pthread'
rm __gpib_trigger__.o gpib_write.o gpib_read.o __gpib_spoll__.o gpib.o __gpib_clrdevice__.o gpib_timeout.o gpib_close.o
pkg: error running `make' for the instrument-control package.
error: called from 'configure_make' in file /Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/share/octave/4.0.3/m/pkg/private/configure_make.m near line 96, column 9
There are a pile of warnings during the build, but they're all for ignored options during compile.
I have successfully installed other packages (control, signal). Could this be a compatibility issue? Ultimately, I need to communicate to a serial device using octave.
Updates:
A student tried the same using Octave 3.8.0 and I tried it with 4.2.0 with the same results.
I tried with -verbose and there doesn't seem to be any more information. There are a bunch of warnings for unused options, but nothing in the (pages of) output that indicate any hints. At the top, I get:
>> pkg install -forge instrument-control -verbose
mkdir (/var/tmp/oct-hJRcYn)
untar (/Users/greg/instrument-control-0.3.0.tar.gz, /var/tmp/oct-hJRcYn)
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 clang++ accepts -g... yes
checking for mkoctfile... /Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/mkoctfile-4.0.3 --verbose
checking for grep that handles long lines and -e... /usr/bin/grep
checking whether install_signal_handlers is in the octave namespace... no
checking whether set_signal_handler is in the octave namespace... no
checking for windows... no
checking how to run the C++ preprocessor... clang++ -E
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 linux/i2c-dev.h usability... no
checking linux/i2c-dev.h presence... no
checking for linux/i2c-dev.h... no
checking dev/iicbus/iic.h usability... no
checking dev/iicbus/iic.h presence... no
checking for dev/iicbus/iic.h... no
checking termios.h usability... yes
checking termios.h presence... yes
checking for termios.h... yes
checking linux/parport.h usability... no
checking linux/parport.h presence... no
checking for linux/parport.h... no
checking linux/ppdev.h usability... no
checking linux/ppdev.h presence... no
checking for linux/ppdev.h... no
checking dev/ppbus/ppi.h usability... no
checking dev/ppbus/ppi.h presence... no
checking for dev/ppbus/ppi.h... no
checking dev/ppbus/ppbconf.h usability... no
checking dev/ppbus/ppbconf.h presence... no
checking for dev/ppbus/ppbconf.h... no
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking winsock2.h usability... no
checking winsock2.h presence... no
checking for winsock2.h... no
checking for library containing getnameinfo... none required
checking gpib/ib.h usability... no
checking gpib/ib.h presence... no
checking for gpib/ib.h... no
checking for rpcgen... yes
checking for library containing clnt_create... none required
checking rpc/rpc.h usability... yes
checking rpc/rpc.h presence... yes
checking for rpc/rpc.h... yes
checking visa/visa.h usability... no
checking visa/visa.h presence... no
checking for visa/visa.h... no
configure: creating ./config.status
config.status: creating octave-wrappers.h
config.status: creating Makefile
config.status: creating gpib/Makefile
config.status: creating tcp/Makefile
config.status: creating udp/Makefile
config.status: creating vxi11/Makefile
config.status: creating usbtmc/Makefile
config.status: creating serial/Makefile
config.status: creating parallel/Makefile
config.status: creating i2c/Makefile
config.status: creating resolvehost/Makefile
config.status: creating config.h
which seems to indicate I have the tools I need. The relevant lines from configure_make are:
if (exist (fullfile (src, "Makefile"), "file"))
[status, output] = shell (sprintf ("%s make --jobs %i --directory '%s'",
scenv, jobs, src), verbose);
if (status != 0)
rmdir (desc.dir, "s");
disp (output);
error ("pkg: error running `make' for the %s package.", desc.name);
endif
endif
Complete output of the command:
pkg install -forge instrument-control -verbose
mkdir (/var/tmp/oct-DzBx8a)
untar (/Users/greg/Dropbox/octave/instrument-control-0.3.0.tar.gz, /var/tmp/oct-DzBx8a)
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 clang++ accepts -g... yes
checking for mkoctfile... /Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/mkoctfile-4.0.3 --verbose
checking for grep that handles long lines and -e... /usr/bin/grep
checking whether install_signal_handlers is in the octave namespace... no
checking whether set_signal_handler is in the octave namespace... no
checking for windows... no
checking how to run the C++ preprocessor... clang++ -E
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 linux/i2c-dev.h usability... no
checking linux/i2c-dev.h presence... no
checking for linux/i2c-dev.h... no
checking dev/iicbus/iic.h usability... no
checking dev/iicbus/iic.h presence... no
checking for dev/iicbus/iic.h... no
checking termios.h usability... yes
checking termios.h presence... yes
checking for termios.h... yes
checking linux/parport.h usability... no
checking linux/parport.h presence... no
checking for linux/parport.h... no
checking linux/ppdev.h usability... no
checking linux/ppdev.h presence... no
checking for linux/ppdev.h... no
checking dev/ppbus/ppi.h usability... no
checking dev/ppbus/ppi.h presence... no
checking for dev/ppbus/ppi.h... no
checking dev/ppbus/ppbconf.h usability... no
checking dev/ppbus/ppbconf.h presence... no
checking for dev/ppbus/ppbconf.h... no
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking winsock2.h usability... no
checking winsock2.h presence... no
checking for winsock2.h... no
checking for library containing getnameinfo... none required
checking gpib/ib.h usability... no
checking gpib/ib.h presence... no
checking for gpib/ib.h... no
checking for rpcgen... yes
checking for library containing clnt_create... none required
checking rpc/rpc.h usability... yes
checking rpc/rpc.h presence... yes
checking for rpc/rpc.h... yes
checking visa/visa.h usability... no
checking visa/visa.h presence... no
checking for visa/visa.h... no
configure: creating ./config.status
config.status: creating octave-wrappers.h
config.status: creating Makefile
config.status: creating gpib/Makefile
config.status: creating tcp/Makefile
config.status: creating udp/Makefile
config.status: creating vxi11/Makefile
config.status: creating usbtmc/Makefile
config.status: creating serial/Makefile
config.status: creating parallel/Makefile
config.status: creating i2c/Makefile
config.status: creating resolvehost/Makefile
config.status: creating config.h
configure:
octave instrument control package is now configured with
BUILD SERIAL: yes
BUILD PARALLEL: no
BUILD I2C: no
BUILD TCP: yes
BUILD UDP: yes
BUILD USBTMC: no
BUILD GPIB: no
BUILD VXI11: yes
BUILD RESOLVEHOST: yes
GPIB LIBS:
VXI11 LIBS:
VXI11 INCLUDE:
VISA LIBS:
TCP LIBS:
/Applications/Xcode.app/Contents/Developer/usr/bin/make -C serial
/Applications/Xcode.app/Contents/Developer/usr/bin/make -C parallel
/Applications/Xcode.app/Contents/Developer/usr/bin/make -C i2c
/Applications/Xcode.app/Contents/Developer/usr/bin/make -C usbtmc
/Applications/Xcode.app/Contents/Developer/usr/bin/make -C tcp
/Applications/Xcode.app/Contents/Developer/usr/bin/make -C udp
/Applications/Xcode.app/Contents/Developer/usr/bin/make -C gpib
/Applications/Xcode.app/Contents/Developer/usr/bin/make -C vxi11
/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/mkoctfile-4.0.3 --verbose -DHAVE_CONFIG_H -c serial_class_lin.cc
/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/mkoctfile-4.0.3 --verbose -DHAVE_CONFIG_H -c parallel_class.cc
/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/mkoctfile-4.0.3 --verbose -DHAVE_CONFIG_H -c i2c_class.cc
/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/mkoctfile-4.0.3 --verbose -DHAVE_CONFIG_H -c usbtmc_class.cc
/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/mkoctfile-4.0.3 --verbose -DHAVE_CONFIG_H -c gpib_class.cc
/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/mkoctfile-4.0.3 --verbose -DHAVE_CONFIG_H -c udp_class.cc
clang++ -c -fPIC -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave/.. -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include -D_THREAD_SAFE -pthread -D_REENTRANT -L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib -lsuitesparseconfig -L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib -lmetis -DHAVE_CONFIG_H parallel_class.cc -o parallel_class.o
rpcgen -M vxi11.x
clang++ -c -fPIC -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave/.. -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include -D_THREAD_SAFE -pthread -D_REENTRANT -L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib -lsuitesparseconfig -L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib -lmetis -DHAVE_CONFIG_H serial_class_lin.cc -o serial_class_lin.o
/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/mkoctfile-4.0.3 --verbose -DHAVE_CONFIG_H -c tcp_class.cc
clang++ -c -fPIC -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave/.. -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include -D_THREAD_SAFE -pthread -D_REENTRANT -L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib -lsuitesparseconfig -L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib -lmetis -DHAVE_CONFIG_H udp_class.cc -o udp_class.o
clang++ -c -fPIC -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave/.. -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include -D_THREAD_SAFE -pthread -D_REENTRANT -L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib -lsuitesparseconfig -L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib -lmetis -DHAVE_CONFIG_H i2c_class.cc -o i2c_class.o
usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/rpcgen infile
clang++ -c -fPIC -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave/.. -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include -D_THREAD_SAFE -pthread -D_REENTRANT -L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib -lsuitesparseconfig -L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib -lmetis -DHAVE_CONFIG_H usbtmc_class.cc -o usbtmc_class.o
clangclang /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/rpcgen [-a][-b][-C][-Dname[=value]] -i size [-I [-K seconds]] [-A][-L][-M toolkit][-N][-T] infile
clangclang++ -c -fPIC -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave/..-I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include -D_THREAD_SAFE -pthread -D_REENTRANT -L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib -lsuitesparseconfig -L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib -lmetis -DHAVE_CONFIG_H gpib_class.cc -o gpib_class.o
: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/rpcgen [-c | -h | -l | -m | -t | -Sc | -Ss] [-o outfile] [infile]
clang++ -c -fPIC -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave/.. -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include -D_THREAD_SAFE -pthread -D_REENTRANT -L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib -lsuitesparseconfig -L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib -lmetis -DHAVE_CONFIG_H tcp_class.cc -o tcp_class.o
: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/rpcgen [-s nettype]* [-o outfile] [infile]
clangclangwarning /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/rpcgen [-n netid]* [-o outfile] [infile]
: warning: : : : -lsuitesparseconfig: 'linker' input unusedwarning-lsuitesparseconfig: 'linker' input unusedwarningclangwarningoptions:
: : :
-A generate svc_caller() function
: -lsuitesparseconfig: 'linker' input unused-a generate all files, including samples
-lsuitesparseconfig: 'linker' input unused-b backward compatibility mode (generates code for SunOS 4.1)
-lsuitesparseconfig: 'linker' input unusedwarning
-c generate XDR routines
: clang-C ANSI C mode
-Dname[=value] define a symbol (same as #define)
: -lsuitesparseconfig: 'linker' input unused
warning-h generate header file
:
-i size size at which to start generating inline code
-lmetis: 'linker' input unused-I generate code for inetd support in server (for SunOS 4.1)
-K seconds server exits after K seconds of inactivity
-l generate client side stubs
clang-L server errors will be printed to syslog
: -m generate server side stubs
warning-n netid generate server code that supports named netid
: clangclangclangclangclang: : warning: warning: warning: : -lmetis: 'linker' input unused-lmetis: 'linker' input unused
-lmetis: 'linker' input unused
:
: warning: warning: -lmetis: 'linker' input unused-lmetis: 'linker' input unused
-lsuitesparseconfig: 'linker' input unused
clang: warning: -lmetis: 'linker' input unused
-N supports multiple arguments and call-by-value
-o outfile name of the output file
-s nettype generate server code that supports named nettype
-Sc generate sample client code that uses remote procedures
-Ss generate sample server code that defines remote procedures
-t generate RPC dispatch table
-T generate code to support RPC dispatch tables
-Y path directory name to find C preprocessor (cpp)
clang: warning: argument unused during compilation: '-L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib'
clang: warning: argument unused during make[1]: compilation: '-L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib'clangclangclangclangclang: : *** [vxi11_clnt.c] Error 1warning: : : warning: warning: warningwarning
argument unused during compilation: '-L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib': argument unused during compilation: '-L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib': argument unused during compilation: '-L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib'
argument unused during compilation: '-L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib'
clang: warning: clangargument unused during compilation: '-L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib': clang
warning: : warningargument unused during compilation: '-L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib':
argument unused during compilation: '-L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib'
clangclang: : warningwarning: : : argument unused during compilation: '-L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib'argument unused during compilation: '-L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib'argument unused during compilation: '-L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib'
...many more warnings...
/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/mkoctfile-4.0.3 --verbose gpib_close.o gpib_class.o -o ../gpib_close.oct
clang++ -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave/.. -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include -D_THREAD_SAFE -pthread -D_REENTRANT -L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib -lsuitesparseconfig -L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib -lmetis -bundle -bundle_loader /Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/octave-4.0.3 -o ../gpib_timeout.oct gpib_timeout.o gpib_class.o -L/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/lib/octave/4.0.3 -L/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/lib -loctinterp -loctave
clang++ -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave/.. -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include -D_THREAD_SAFE -pthread -D_REENTRANT -L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib -lsuitesparseconfig -L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib -lmetis -bundle -bundle_loader /Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/octave-4.0.3 -o ../gpib_write.oct gpib_write.o gpib_class.o -L/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/lib/octave/4.0.3 -L/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/lib -loctinterp -loctave
/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/mkoctfile-4.0.3 --verbose gpib_read.o gpib_class.o-o ../gpib_read.oct
clang++ -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave/.. -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include -D_THREAD_SAFE -pthread -D_REENTRANT -L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib -lsuitesparseconfig -L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib -lmetis -bundle -bundle_loader /Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/octave-4.0.3 -o ../gpib_close.oct gpib_close.o gpib_class.o -L/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/lib/octave/4.0.3 -L/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/lib -loctinterp -loctave
clang: warning: argument unused during compilation: '-pthread'
clang++ -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave/.. -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include -D_THREAD_SAFE -pthread -D_REENTRANT -L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib -lsuitesparseconfig -L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib -lmetis -bundle -bundle_loader /Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/octave-4.0.3 -o ../gpib_read.oct gpib_read.o gpib_class.o -L/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/lib/octave/4.0.3 -L/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/lib -loctinterp -loctave
clangclang: /Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/mkoctfile-4.0.3 --verbose __gpib_spoll__.o gpib_class.o -o ../__gpib_spoll__.oct
warning: clang: warning: argument unused during compilation: '-pthread'argument unused during compilation: '-pthread'
: warning: argument unused during compilati/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/mkoctfile-4.0.3 --verbose __gpib_trigger__.o gpib_class.o -o ../__gpib_trigger__.oct
on: '-pthread'clang++ -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave/.. -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include -D_THREAD_SAFE -pthread -D_REENTRANT -L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib -lsuitesparseconfig -L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib -lmetis -bundle -bundle_loader /Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/octave-4.0.3 -o ../__gpib_spoll__.oct __gpib_spoll__.o gpib_class.o -L/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/lib/octave/4.0.3 -L/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/lib -loctinterp -loctave
clang: warniclang++ -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave/.. -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include -D_THREAD_SAFE -pthread -D_REENTRANT -L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib -lsuitesparseconfig -L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib -lmetis -bundle -bundle_loader /Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/octave-4.0.3 -o ../__gpib_trigger__.oct __gpib_trigger__.o gpib_class.o -L/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/lib/octave/4.0.3 -L/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/lib -loctinterp -loctave
ngclang: : argument unused during compilation: '-pthread'warning
: argument unused during compilation: '-pthread'
1 warning generated.
/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/mkoctfile-4.0.3 --verbose __udp_properties__.o udp_class.o -o ../__udp_properties__.oct
clang: warning: argument unused during compilation: '-pthread'
clang++ -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave/.. -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include -D_THREAD_SAFE -pthread -D_REENTRANT -L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib -lsuitesparseconfig -L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib -lmetis -bundle -bundle_loader /Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/octave-4.0.3 -o ../__udp_properties__.oct __udp_properties__.o udp_class.o -L/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/lib/octave/4.0.3 -L/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/lib -loctinterp -loctave
clang: warning: argument unused during compilation: '-pthread'
rm udp.o udp_timeout.o udp_close.o __udp_properties__.o udp_write.o udp_read.o
/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/mkoctfile-4.0.3 --verbose __gpib_clrdevice__.o gpib_class.o -o ../__gpib_clrdevice__.oct
clang++ -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave/.. -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include/octave-4.0.3/octave -I/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/include -D_THREAD_SAFE -pthread -D_REENTRANT -L/Applications/Octave.app/Contents/Resources/usr/opt/suite-sparse/lib -lsuitesparseconfig -L/Applications/Octave.app/Contents/Resources/usr/opt/metis/lib -lmetis -bundle -bundle_loader /Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/bin/octave-4.0.3 -o ../__gpib_clrdevice__.oct __gpib_clrdevice__.o gpib_class.o -L/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/lib/octave/4.0.3 -L/Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/lib -loctinterp -loctave
clang: warning: argument unused during compilation: '-pthread'
rm __gpib_trigger__.o gpib_write.o gpib_read.o __gpib_spoll__.o gpib.o __gpib_clrdevice__.o gpib_timeout.o gpib_close.o
pkg: error running `make' for the instrument-control package.
error: called from 'configure_make' in file /Applications/Octave.app/Contents/Resources/usr/Cellar/octave/4.0.3/share/octave/4.0.3/m/pkg/private/configure_make.m near line 96, column 9
While it is not a full solution to this problem, this could be a workaround if the VXI-11 interface is not needed. For instance, this worked for me to read serial data form an Arduino Micro.
After reporting the bug in the GNU Octave's bug tracker Savannah (see here), I was able to install the octave instrument-control package (see comment #3) in:
Octave 4.4.1
macOS Mojave
Apparently, as it can also be seen in the above provided output, the error occurs when running
rpcgen -M vxi11.x
since the rpcgen appears not to have the -M option (needed for the installation, otherwise it does not compile). I tried installing a newer version of rpcgen for macOS that included a -M (see e.g. rpcgen-mt here and here), but it didn't work. By omitting the installation of vxi11 (VXI-11 interface), I was finally able to install the instrument-control package.
Here are the steps I followed for this solution:
Download the instrument-control package from Octave Forge (e.g. here).
Expand the downloaded *.tar.gz file.
Open the Makefile.in inside src/ with your favourite text editor.
There should be a line (line 2 in my case) indicating the subdirectories to be installed
(e.g. SUBDIRS = serial parallel i2c usbtmc tcp udp gpib vxi11 resolvehost hwinfo)
Remove vxi11 from the list.
(i.e. SUBDIRS = serial parallel i2c usbtmc tcp udp gpib resolvehost hwinfo)
Save changes.
Generate the new .tar.gz file
$ tar -czf instrument-control-0.3.1.tar.gz instrument-control-0.3.1/
(with the appropriate numbers of the package version).
Inside Octave, while in the same directory of the above generated .tar.gz file, run:
> pkg install instrument-control-0.3.1.tar.gz -verbose
(again with the appropriate numbers of the package version).
After the installation some warnings may appear mainly due to the fact that vxi11 was omitted.
warning: autoload: 'vxi11.oct' is not an absolute filename
warning: autoload: 'vxi11.oct' is not an absolute filename
warning: autoload: 'vxi11.oct' is not an absolute filename
warning: autoload: 'vxi11.oct' is not an absolute filename
For information about changes from previous versions of the instrument-control package, run 'news instrument-control'.
However, the output of > pkg list should include the instrument-control package (amongst any others installed packages):
Package Name | Version | Installation directory
--------------------+---------+-----------------------
control | 3.1.0 | /Users/Xavi/octave/control-3.1.0
instrument-control | 0.3.1 | /Users/Xavi/octave/instrument-control-0.3.1
signal | 1.4.0 | /Users/Xavi/octave/signal-1.4.0
symbolic | 2.7.1 | /Users/Xavi/octave/symbolic-2.7.1
In addition, some warnings may also appear every time the instrument-control package is loaded for the first time (> pkg load instrument-control). This warnings again refer to the missing installation of vxi11.
Despite of these warnings, I have been able to correctly read serial data form an Arduino Micro.
SPro can be downloaded here,and it's installed by ./configure, make, make install. However, ./configure and make both arouse errors.
First, run ./configure, get the following warnings:
Try /large_dsk/share/upload/spro-5.0/spro-5.0/auxdir/missing --help' for more information
configure: WARNING: 'missing' script is too old or missing
checking for gawk... no
The total output is as following:
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
/large_dsk/share/upload/spro-5.0/spro-5.0/auxdir/missing: Unknown `--run' option
Try `/large_dsk/share/upload/spro-5.0/spro-5.0/auxdir/missing --help' for more information
configure: WARNING: `missing' script is too old or missing
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking for ranlib... ranlib
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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 ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ANSI C... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for AIX... no
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking for library containing strerror... none required
checking for function prototypes... yes
checking for string.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking whether byte ordering is bigendian... no
checking for size_t... yes
checking for char... yes
checking size of char... 1
checking for short... yes
checking size of short... 2
checking for long... yes
checking size of long... 8
checking for ANSI C header files... (cached) yes
checking whether time.h and sys/time.h may both be included... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking for stdlib.h... (cached) yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking for string.h... (cached) yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for vprintf... yes
checking for _doprnt... no
configure: checking for gcc warning options...
... -Wbad-function-cast
... -Wcast-align
... -Wmissing-declarations
... -Wmissing-prototypes
... -Wnested-externs
... -Wpointer-arith
... -Wshadow
... -Wstrict-prototypes
... -Wwrite-strings
checking if malloc debugging is wanted... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating doc/Makefile
config.status: creating auxdir/Makefile
config.status: creating test/Makefile
config.status: creating test/ref/Makefile
config.status: creating test/dat/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
Second, when run the make, get the following errors:
I searched this error, and get the method that add -lm in gcc command, but seemly it doesn't work.
And the total ouput is as following:
So should I install some libs first or the gcc version is not right? my gcc version is gcc 5.4.0.
make all-recursive
make[1]: Entering directory '/large_dsk/share/upload/spro-5.0/spro-5.0'
Making all in doc
make[2]: Entering directory '/large_dsk/share/upload/spro-5.0/spro-5.0/doc'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/large_dsk/share/upload/spro-5.0/spro-5.0/doc'
Making all in auxdir
make[2]: Entering directory '/large_dsk/share/upload/spro-5.0/spro-5.0/auxdir'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/large_dsk/share/upload/spro-5.0/spro-5.0/auxdir'
Making all in test
make[2]: Entering directory '/large_dsk/share/upload/spro-5.0/spro-5.0/test'
Making all in ref
make[3]: Entering directory '/large_dsk/share/upload/spro-5.0/spro-5.0/test/ref'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/large_dsk/share/upload/spro-5.0/spro-5.0/test/ref'
Making all in dat
make[3]: Entering directory '/large_dsk/share/upload/spro-5.0/spro-5.0/test/dat'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/large_dsk/share/upload/spro-5.0/spro-5.0/test/dat'
make[3]: Entering directory '/large_dsk/share/upload/spro-5.0/spro-5.0/test'
make[3]: Nothing to be done for 'all-am'.
make[3]: Leaving directory '/large_dsk/share/upload/spro-5.0/spro-5.0/test'
make[2]: Leaving directory '/large_dsk/share/upload/spro-5.0/spro-5.0/test'
make[2]: Entering directory '/large_dsk/share/upload/spro-5.0/spro-5.0'
if gcc -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -MT sig.o -MD -MP -MF ".deps/sig.Tpo" -c -o sig.o sig.c; \
then mv -f ".deps/sig.Tpo" ".deps/sig.Po"; else rm -f ".deps/sig.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -MT spf.o -MD -MP -MF ".deps/spf.Tpo" -c -o spf.o spf.c; \
then mv -f ".deps/spf.Tpo" ".deps/spf.Po"; else rm -f ".deps/spf.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -MT header.o -MD -MP -MF ".deps/header.Tpo" -c -o header.o header.c; \
then mv -f ".deps/header.Tpo" ".deps/header.Po"; else rm -f ".deps/header.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -MT misc.o -MD -MP -MF ".deps/misc.Tpo" -c -o misc.o misc.c; \
then mv -f ".deps/misc.Tpo" ".deps/misc.Po"; else rm -f ".deps/misc.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -MT lpc.o -MD -MP -MF ".deps/lpc.Tpo" -c -o lpc.o lpc.c; \
then mv -f ".deps/lpc.Tpo" ".deps/lpc.Po"; else rm -f ".deps/lpc.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -MT convert.o -MD -MP -MF ".deps/convert.Tpo" -c -o convert.o convert.c; \
then mv -f ".deps/convert.Tpo" ".deps/convert.Po"; else rm -f ".deps/convert.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -MT fft.o -MD -MP -MF ".deps/fft.Tpo" -c -o fft.o fft.c; \
then mv -f ".deps/fft.Tpo" ".deps/fft.Po"; else rm -f ".deps/fft.Tpo"; exit 1; fi
rm -f libspro.a
ar cru libspro.a sig.o spf.o header.o misc.o lpc.o convert.o fft.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libspro.a
if gcc -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -MT scopy.o -MD -MP -MF ".deps/scopy.Tpo" -c -o scopy.o scopy.c; \
then mv -f ".deps/scopy.Tpo" ".deps/scopy.Po"; else rm -f ".deps/scopy.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I. -g -O2 -MT gggetopt.o -MD -MP -MF ".deps/gggetopt.Tpo" -c -o gggetopt.o gggetopt.c; \
then mv -f ".deps/gggetopt.Tpo" ".deps/gggetopt.Po"; else rm -f ".deps/gggetopt.Tpo"; exit 1; fi
gggetopt.c: In function \u2018_getopt_long\u2019:
gggetopt.c:442:12: warning: implicit declaration of function \u2018strcmp\u2019 [-Wimplicit-function-declaration]
if ( strcmp(optarg, "--") == 0 ) {
^
gcc -g -O2 -o scopy scopy.o gggetopt.o -lm -L. -lspro
./libspro.a(misc.o): In function `spf_buf_normalize':
/large_dsk/share/upload/spro-5.0/spro-5.0/misc.c:278: undefined reference to `sqrt'
/large_dsk/share/upload/spro-5.0/spro-5.0/misc.c:187: undefined reference to `sqrt'
./libspro.a(misc.o): In function `set_lifter':
/large_dsk/share/upload/spro-5.0/spro-5.0/misc.c:408: undefined reference to `sin'
./libspro.a(misc.o): In function `sig_normalize':
/large_dsk/share/upload/spro-5.0/spro-5.0/misc.c:431: undefined reference to `sqrt'
./libspro.a(misc.o): In function `set_sig_win':
/large_dsk/share/upload/spro-5.0/spro-5.0/misc.c:464: undefined reference to `cos'
/large_dsk/share/upload/spro-5.0/spro-5.0/misc.c:479: undefined reference to `cos'
/large_dsk/share/upload/spro-5.0/spro-5.0/misc.c:479: undefined reference to `cos'
/large_dsk/share/upload/spro-5.0/spro-5.0/misc.c:471: undefined reference to `cos'
collect2: error: ld returned 1 exit status
Makefile:353: recipe for target 'scopy' failed
make[2]: *** [scopy] Error 1
make[2]: Leaving directory '/large_dsk/share/upload/spro-5.0/spro-5.0'
Makefile:432: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/large_dsk/share/upload/spro-5.0/spro-5.0'
Makefile:236: recipe for target 'all' failed
make: *** [all] Error 2
I think the build script is just wrong:
gcc -g -O2 -o scopy scopy.o gggetopt.o -lm -L. -lspro
Since -lspro uses functions from -lm, it has to come first. See this answer for some background.
I encountered the same error as you did. I wanted to installed spro 4.0 and failed.
I have been tried a lot of methods like updating the gcc,and install different version gcc but it didn't work anymore.I think the reason of this error is that installing spro 4.0 needs a old version gcc like g++-4.4.
So I solved this problem as follow:
1.first install g++-4.4,
we maybe can't install g++-4.4 in directly,so we have to install or update by the command as follow:
$sudo add-apt-repository ppa:ubuntu-toolchain-r/test
$sudo apt-get update
$sudo apt-get install gcc-4.4 g++-4.4 g++-4.4-multilib
2.when installed g++-4.4 successfully, we enter the spro4.0 directory and run the install command,to prevent the permission of the installation,I suggest that we run in root or sudo:
# export CC=gcc-4.4
# ./configure && make && make install
Please don't hesitate to contact me if you have any questions.
I am trying to make a tool called seqpp. But I get this error:
/bin/sh ../libtool --tag=F77 --mode=compile -c -o fcdiv.lo fcdiv.f
libtool: compile: unrecognized option `-c'
libtool: compile: Try `libtool --help' for more information.
I work on MacOSx 10.9.5 Mavericks
I have thought of 2 problems:
an absence of fortran compiler,
or a problem with libtool package.
So I installed gfortran by reinstalling gcc compiler using Macports : sudo port install gcc46 +gfortran. And I reinstalled libtool using MacPorts. I also installed the last version of developper tools installed, just in case.
libtool seems to be correctly installed:
$ which libtool
/usr/bin/libtool
I do not really know how to check the installation for gfortran. And it might still not be ok; as you can see in log: checking for f77... no
Is that the right problem? If yes, how to fix it?
Thanks in advance for your precious help!
Here is the whole log of the installation ("./configure" followed by "make" commands):
$ ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for gawk... (cached) awk
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... no
checking for g95... no
checking for xlf95... no
checking for f95... no
checking for fort... no
checking for ifort... no
checking for ifc... no
checking for efc... no
checking for pgf95... no
checking for lf95... no
checking for ftn... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether accepts -g... no
checking for a BSD-compatible install... /usr/bin/install -c
checking whether ln -s works... yes
checking build system type... i386-apple-darwin13.4.0
checking host system type... i386-apple-darwin13.4.0
checking for gcc... gcc
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 dependency style of gcc... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /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)... /opt/local/bin/nm
checking the name lister (/opt/local/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 how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /opt/local/bin/nm output from gcc object... ok
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking how to run the C preprocessor... gcc -E
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 for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
checking for g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... no
checking for g95... no
checking for xlf95... no
checking for f95... no
checking for fort... no
checking for ifort... no
checking for ifc... no
checking for efc... no
checking for pgf95... no
checking for lf95... no
checking for ftn... no
checking whether we are using the GNU Fortran 77 compiler... (cached) no
checking whether accepts -g... (cached) no
checking for objdir... .libs
rm: conftest.dSYM: is a directory
checking if gcc supports -fno-rtti -fno-exceptions... yes
checking for gcc option to produce PIC... -fno-common -DPIC
checking if gcc PIC flag -fno-common -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin13.4.0 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... yes
checking for ld used by 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 g++ linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fno-common -DPIC
checking if g++ PIC flag -fno-common -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin13.4.0 dyld
checking how to hardcode library paths into programs... immediate
checking for gsl-config... /usr/local/bin/gsl-config
checking for doxygen... no
checking libintl.h usability... no
checking libintl.h presence... no
checking for libintl.h... no
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking for getopt.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for strchr... yes
checking for strcspn... yes
checking for strrchr... yes
checking for strtol... yes
checking for main in -lm... yes
checking for ANSI C header files... (cached) yes
checking for an ANSI C-conforming const... (cached) yes
checking for inline... inline
checking whether make sets $(MAKE)... (cached) yes
configure: creating ./config.status
config.status: creating seqpp.spec
config.status: creating Makefile
config.status: creating seqpp/Makefile
config.status: creating doc/Makefile
config.status: creating doc/doxyfiles/config.dox
config.status: creating doc/doxyfiles/header.html
config.status: creating doc/doxyfiles/footer.html
config.status: creating doc/html/Makefile
config.status: creating doc/man/Makefile
config.status: creating argtable2/Makefile
config.status: creating src/Makefile
config.status: creating alphabet/Makefile
config.status: creating data/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
configure: WARNING: "Note that XML Library libxml2 NOT FOUND or XML Modules NOT ACTIVATED by --enable-xml => XML output disabled."
pc17:seqpp-4.2.0 iryna$ make
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive
Making all in seqpp
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. `/usr/local/bin/gsl-config --cflags` `` -O3 -MT Coder.lo -MD -MP -MF .deps/Coder.Tpo -c -o Coder.lo Coder.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -O3 -MT Coder.lo -MD -MP -MF .deps/Coder.Tpo -c Coder.cc -fno-common -DPIC -o .libs/Coder.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -O3 -MT Coder.lo -MD -MP -MF .deps/Coder.Tpo -c Coder.cc -o Coder.o >/dev/null 2>&1
mv -f .deps/Coder.Tpo .deps/Coder.Plo
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. `/usr/local/bin/gsl-config --cflags` `` -O3 -MT arnoldi.lo -MD -MP -MF .deps/arnoldi.Tpo -c -o arnoldi.lo arnoldi.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -O3 -MT arnoldi.lo -MD -MP -MF .deps/arnoldi.Tpo -c arnoldi.cc -fno-common -DPIC -o .libs/arnoldi.o
arnoldi.cc:218:51: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
cerr<<"arnoldi: no convergence, too many it<E9>rations !"<<endl;
^~~~
arnoldi.cc:482:51: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
cerr<<"arnoldi: no convergence, too many it<E9>rations !"<<endl;
^~~~
arnoldi.cc:744:51: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
cerr<<"arnoldi: no convergence, too many it<E9>rations !"<<endl;
^~~~
arnoldi.cc:1009:51: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
cerr<<"arnoldi: no convergence, too many it<E9>rations !"<<endl;
^~~~
4 warnings generated.
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -O3 -MT arnoldi.lo -MD -MP -MF .deps/arnoldi.Tpo -c arnoldi.cc -o arnoldi.o >/dev/null 2>&1
mv -f .deps/arnoldi.Tpo .deps/arnoldi.Plo
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. `/usr/local/bin/gsl-config --cflags` `` -O3 -MT Sequence.lo -MD -MP -MF .deps/Sequence.Tpo -c -o Sequence.lo Sequence.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -O3 -MT Sequence.lo -MD -MP -MF .deps/Sequence.Tpo -c Sequence.cc -fno-common -DPIC -o .libs/Sequence.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -O3 -MT Sequence.lo -MD -MP -MF .deps/Sequence.Tpo -c Sequence.cc -o Sequence.o >/dev/null 2>&1
mv -f .deps/Sequence.Tpo .deps/Sequence.Plo
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. `/usr/local/bin/gsl-config --cflags` `` -O3 -MT PrimarySequence.lo -MD -MP -MF .deps/PrimarySequence.Tpo -c -o PrimarySequence.lo PrimarySequence.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -O3 -MT PrimarySequence.lo -MD -MP -MF .deps/PrimarySequence.Tpo -c PrimarySequence.cc -fno-common -DPIC -o .libs/PrimarySequence.o
PrimarySequence.cc:19:26: warning: comparison of unsigned expression < 0 is
always false [-Wtautological-compare]
if ( ( beg>stop )||(beg<0)||(stop>=_length) ){
~~~^~
PrimarySequence.cc:36:26: warning: comparison of unsigned expression < 0 is
always false [-Wtautological-compare]
if ( ( beg>stop )||(beg<0)||(stop>=_length) ){
~~~^~
2 warnings generated.
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -O3 -MT PrimarySequence.lo -MD -MP -MF .deps/PrimarySequence.Tpo -c PrimarySequence.cc -o PrimarySequence.o >/dev/null 2>&1
mv -f .deps/PrimarySequence.Tpo .deps/PrimarySequence.Plo
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. `/usr/local/bin/gsl-config --cflags` `` -O3 -MT SequenceSet.lo -MD -MP -MF .deps/SequenceSet.Tpo -c -o SequenceSet.lo SequenceSet.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -O3 -MT SequenceSet.lo -MD -MP -MF .deps/SequenceSet.Tpo -c SequenceSet.cc -fno-common -DPIC -o .libs/SequenceSet.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -O3 -MT SequenceSet.lo -MD -MP -MF .deps/SequenceSet.Tpo -c SequenceSet.cc -o SequenceSet.o >/dev/null 2>&1
mv -f .deps/SequenceSet.Tpo .deps/SequenceSet.Plo
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. `/usr/local/bin/gsl-config --cflags` `` -O3 -MT PhasedMarkov.lo -MD -MP -MF .deps/PhasedMarkov.Tpo -c -o PhasedMarkov.lo PhasedMarkov.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -O3 -MT PhasedMarkov.lo -MD -MP -MF .deps/PhasedMarkov.Tpo -c PhasedMarkov.cc -fno-common -DPIC -o .libs/PhasedMarkov.o
In file included from PhasedMarkov.cc:1:
../seqpp/PhasedMarkov.h:31:17: warning: using directive refers to
implicitly-defined namespace 'std'
using namespace std;
^
PhasedMarkov.cc:63:20: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
cerr<<"\"# Phase n<B0>\" line missing or mispositionned"<<endl;
^~~~
PhasedMarkov.cc:935:46: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
cerr<<"arnoldi: no convergence, too many it<E9>rations !"<<endl;
^~~~
PhasedMarkov.cc:1396:5: warning: add explicit braces to avoid dangling else
[-Wdangling-else]
else{
^
PhasedMarkov.cc:1413:4: warning: add explicit braces to avoid dangling else
[-Wdangling-else]
else{
^
PhasedMarkov.cc:1426:2: warning: add explicit braces to avoid dangling else
[-Wdangling-else]
else{
^
PhasedMarkov.cc:1458:6: warning: add explicit braces to avoid dangling else
[-Wdangling-else]
else{
^
PhasedMarkov.cc:1619:70: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
...PhasedMarkov::distVarTot\n, Pi ou Mu ne sont pas d<E9>finis pour une de...
^~~~
PhasedMarkov.cc:1677:19: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
Out << "# Phase n<B0>" << p <<endl;
^~~~
9 warnings generated.
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -O3 -MT PhasedMarkov.lo -MD -MP -MF .deps/PhasedMarkov.Tpo -c PhasedMarkov.cc -o PhasedMarkov.o >/dev/null 2>&1
mv -f .deps/PhasedMarkov.Tpo .deps/PhasedMarkov.Plo
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. `/usr/local/bin/gsl-config --cflags` `` -O3 -MT Markov.lo -MD -MP -MF .deps/Markov.Tpo -c -o Markov.lo Markov.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -O3 -MT Markov.lo -MD -MP -MF .deps/Markov.Tpo -c Markov.cc -fno-common -DPIC -o .libs/Markov.o
In file included from Markov.cc:1:
In file included from ../seqpp/Markov.h:31:
../seqpp/PhasedMarkov.h:31:17: warning: using directive refers to
implicitly-defined namespace 'std'
using namespace std;
^
1 warning generated.
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -O3 -MT Markov.lo -MD -MP -MF .deps/Markov.Tpo -c Markov.cc -o Markov.o >/dev/null 2>&1
mv -f .deps/Markov.Tpo .deps/Markov.Plo
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. `/usr/local/bin/gsl-config --cflags` `` -O3 -MT Translator.lo -MD -MP -MF .deps/Translator.Tpo -c -o Translator.lo Translator.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -O3 -MT Translator.lo -MD -MP -MF .deps/Translator.Tpo -c Translator.cc -fno-common -DPIC -o .libs/Translator.o
Translator.cc:183:37: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
cout<<_iter_si->first<<" est associ<E9> <E0> "
^~~~ ~~~~
Translator.cc:190:37: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
cout<<_iter_ci->first<<" est associ<E9> <E0> "
^~~~ ~~~~
Translator.cc:202:37: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
cout<<_iter_si->first<<" est associ<E9> <E0> "
^~~~ ~~~~
Translator.cc:207:17: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
cout<<"Compl<E9>mentaire"<<endl;
^~~~
Translator.cc:211:37: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
cout<<_iter_si->first<<" est associ<E9> <E0> "
^~~~ ~~~~
Translator.cc:218:28: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
cout<<i<<" est associ<E9> <E0> "
^~~~ ~~~~
Translator.cc:223:28: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
cout<<i<<" est associ<E9> <E0> "
^~~~ ~~~~
Translator.cc:353:37: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
cout<<_iter_si->first<<" est associ<E9> <E0> "
^~~~ ~~~~
Translator.cc:360:37: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
cout<<_iter_ci->first<<" est associ<E9> <E0> "
^~~~ ~~~~
Translator.cc:372:37: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
cout<<_iter_si->first<<" est associ<E9> <E0> "
^~~~ ~~~~
Translator.cc:379:28: warning: illegal character encoding in string literal
[-Winvalid-source-encoding]
cout<<i<<" est associ<E9> <E0> "
^~~~ ~~~~
11 warnings generated.
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -O3 -MT Translator.lo -MD -MP -MF .deps/Translator.Tpo -c Translator.cc -o Translator.o >/dev/null 2>&1
mv -f .deps/Translator.Tpo .deps/Translator.Plo
/bin/sh ../libtool --tag=F77 --mode=compile -c -o fcdiv.lo fcdiv.f
libtool: compile: unrecognized option `-c'
libtool: compile: Try `libtool --help' for more information.
make[2]: *** [fcdiv.lo] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
Actually I figured out the problem: it was indeed due to absence of fortran compiler. As I have told, I had downloaded from Macports a gcc compiler containing fortran with:
sudo port install gcc46 +gfortran
Then I had to set this compiler as my default compiler:
1)install gcc_select from Macports
sudo port install gcc_select
2)view all gcc compilers and set one of them as compiler by default (my compiler is mp-gcc46) :
port select --list gcc
sudo port select --set gcc mp-gcc46
3)you can check that the compiler has been modified:
gcc --version
That's it, I hope it will help somebody
I need hunspell. I am a windows user. I am using win 7 ultimate English.
OS Name Microsoft Windows 7 Ultimate
Version 6.1.7601 Service Pack 1 Build 7601
Other OS Description Not Available
OS Manufacturer Microsoft Corporation
System Name NURAS-PC
System Manufacturer Sony Corporation
System Model VPCW21M1E
System Type x64-based PC
Processor Intel(R) Atom(TM) CPU N450 # 1.66GHz, 1666 Mhz, 1 Core(s), 2 Logical Processor(s)
BIOS Version/Date INSYDE R0240E2, 07-Dec-09
SMBIOS Version 2.6
Windows Directory C:\Windows
System Directory C:\Windows\system32
Boot Device \Device\HarddiskVolume1
Locale United States
Hardware Abstraction Layer Version = "6.1.7601.17514"
User Name nuras-PC\nuras
Time Zone Turkey Daylight Time
Installed Physical Memory (RAM) 2.00 GB
Total Physical Memory 1.99 GB
Available Physical Memory 704 MB
Total Virtual Memory 4.23 GB
Available Virtual Memory 1.84 GB
Page File Space 2.24 GB
Page File C:\pagefile.sys
Yesterday I installed Cygwin x86 all packages written in hunspell read me.
2. Compiling in Cygwin environment
make
gcc-g++ development package
mingw development package (for cygwin.dll free native Windows compilation)
ncurses, readline (for user interface)
iconv (character conversion)
I selected nearly all dev and util packages
firstly I pasted my "C:\cygwin\bin\cygwin1.dll" to "c:\Windows\system32\"
the first time pushed the Cygwin console wrote the command "mkdir dene"
then I added the path the windows path
my downloaded hunspell I unzipped two times with 7zip and copied pasted to under "dene" directory
then pushed Cygwin console
nuras#nuras-PC ~
$ cd dene
nuras#nuras-PC ~/dene
$ ls
hunspell-1.3.2
nuras#nuras-PC ~/dene
$ cd hunspell-1.3.2
nuras#nuras-PC ~/dene/hunspell-1.3.2
$ ./configure --with-ui
checking build system type... i686-pc-cygwin
checking host system type... i686-pc-cygwin
checking target system type... i686-pc-cygwin
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.exe
checking for suffix of executables... .exe
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 g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
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 dependency style of gcc... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/i686-pc-cygwin/bin/ld.exe
checking if the linker (/usr/i686-pc-cygwin/bin/ld.exe) 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 whether ln -s works... yes
checking the maximum length of command line arguments... 8192
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/i686-pc-cygwin/bin/ld.exe option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... file_magic ^x86 archive import|^x86 DLL
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking how to run the C preprocessor... gcc -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 for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -DDLL_EXPORT -DPIC
checking if gcc PIC flag -DDLL_EXPORT -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/i686-pc-cygwin/bin/ld.exe) supports shared libraries... yes
checking whether -lc should be explicitly linked in... yes
checking dynamic linker characteristics... Win32 ld.exe
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... yes
checking for ld used by g++... /usr/i686-pc-cygwin/bin/ld.exe
checking if the linker (/usr/i686-pc-cygwin/bin/ld.exe) is GNU ld... yes
checking whether the g++ linker (/usr/i686-pc-cygwin/bin/ld.exe) supports shared libraries... yes
checking for g++ option to produce PIC... -DDLL_EXPORT -DPIC
checking if g++ PIC flag -DDLL_EXPORT -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/i686-pc-cygwin/bin/ld.exe) supports shared libraries... yes
checking dynamic linker characteristics... Win32 ld.exe
checking how to hardcode library paths into programs... immediate
checking for as... as
checking for dlltool... dlltool
checking for objdump... (cached) objdump
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking libintl.h usability... no
checking libintl.h presence... no
checking for libintl.h... no
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking for unistd.h... (cached) yes
checking error.h usability... yes
checking error.h presence... yes
checking for error.h... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for error_at_line... yes
checking for ANSI C header files... (cached) yes
checking for memchr... yes
checking for setlocale... yes
checking for strchr... yes
checking for strstr... yes
checking whether NLS is requested... yes
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 size_t... yes
checking for stdint.h... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking whether integer division by zero raises SIGFPE... yes
checking for inttypes.h... yes
checking for unsigned long long int... yes
checking for inttypes.h... (cached) yes
checking whether the inttypes.h PRIxNN macros are broken... no
checking 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 ld used by GCC... /usr/i686-pc-cygwin/bin/ld.exe
checking if the linker (/usr/i686-pc-cygwin/bin/ld.exe) is GNU ld... yes
checking for shared library run path origin... done
checking whether imported symbols can be declared weak... yes
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking for pthread_kill in -lpthread... yes
checking for pthread_rwlock_t... yes
checking for multithread API to use... posix
checking argz.h usability... yes
checking argz.h presence... yes
checking for argz.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... 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... yes
checking for munmap... yes
checking for stpcpy... yes
checking for strcasecmp... yes
checking for strdup... yes
checking for strtoul... yes
checking for tsearch... yes
checking for argz_count... yes
checking for argz_stringify... yes
checking for argz_next... yes
checking for __fsetlocking... no
checking whether feof_unlocked is declared... no
checking whether fgets_unlocked is declared... no
checking for iconv... yes
checking for working iconv... yes
checking how to link with libiconv... -liconv
checking for iconv declaration... install-shextern 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... no
checking for long long int... 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... no
checking for CFLocaleCopyCurrent... no
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... yes
checking for setenv... yes
checking for setlocale... (cached) 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... yes
checking for LC_MESSAGES... yes
checking for windres... windres
checking for CFPreferencesCopyAppValue... (cached) no
checking for CFLocaleCopyCurrent... (cached) no
checking whether included gettext is requested... no
checking for GNU gettext in libc... no
checking for GNU gettext in libintl... no
checking whether to use NLS... yes
checking where the gettext function comes from... included intl directory
checking for tparm in -lncursesw... yes
Compiling with curses user interface.
configure: creating ./config.status
config.status: creating Makefile
config.status: creating hunspell.pc
config.status: creating man/Makefile
config.status: creating man/hu/Makefile
config.status: creating intl/Makefile
config.status: creating po/Makefile.in
config.status: creating m4/Makefile
config.status: creating src/Makefile
config.status: creating src/hunspell/Makefile
config.status: creating src/hunspell/hunvisapi.h
config.status: creating src/parsers/Makefile
config.status: creating src/tools/Makefile
config.status: creating src/win_api/Makefile
config.status: creating tests/Makefile
config.status: creating tests/suggestiontest/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing po-directories commands
config.status: creating po/POTFILES
config.status: creating po/Makefile
nuras#nuras-PC ~/dene/hunspell-1.3.2
$ make
make all-recursive
make[1]: Entering directory '/home/nuras/dene/hunspell-1.3.2'
Making all in intl
make[2]: Entering directory '/home/nuras/dene/hunspell-1.3.2/intl'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/home/nuras/dene/hunspell-1.3.2/intl'
Making all in po
make[2]: Entering directory '/home/nuras/dene/hunspell-1.3.2/po'
make[2]: Leaving directory '/home/nuras/dene/hunspell-1.3.2/po'
Making all in src
make[2]: Entering directory '/home/nuras/dene/hunspell-1.3.2/src'
Making all in hunspell
make[3]: Entering directory '/home/nuras/dene/hunspell-1.3.2/src/hunspell'
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT affentry.lo -MD -MP -MF .deps/affentry.Tpo -c -o affentry.lo affentry.cxx
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT affentry.lo -MD -MP -MF .deps/affentry.Tpo -c affentry.cxx -DDLL_EXPORT -DPIC -o .libs/affentry.o
In file included from affentry.cxx:9:0:
affentry.hxx:30:105: warning: converting to non-pointer type ‘short unsigned int’ from NULL [-Wconversion-null]
struct hentry * check_twosfx(const char * word, int len, char in_compound, const FLAG needflag = NULL);
^
affentry.hxx:93:114: warning: converting to non-pointer type ‘short unsigned int’ from NULL [-Wconversion-null]
struct hentry * check_twosfx(const char * word, int len, int optflags, PfxEntry* ppfx, const FLAG needflag = NULL);
^
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT affentry.lo -MD -MP -MF .deps/affentry.Tpo -c affentry.cxx -o affentry.o >/dev/null 2>&1
mv -f .deps/affentry.Tpo .deps/affentry.Plo
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT affixmgr.lo -MD -MP -MF .deps/affixmgr.Tpo -c -o affixmgr.lo affixmgr.cxx
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT affixmgr.lo -MD -MP -MF .deps/affixmgr.Tpo -c affixmgr.cxx -DDLL_EXPORT -DPIC -o .libs/affixmgr.o
In file included from affixmgr.cxx:12:0:
affentry.hxx:30:105: warning: converting to non-pointer type ‘short unsigned int’ from NULL [-Wconversion-null]
struct hentry * check_twosfx(const char * word, int len, char in_compound, const FLAG needflag = NULL);
^
affentry.hxx:93:114: warning: converting to non-pointer type ‘short unsigned int’ from NULL [-Wconversion-null]
struct hentry * check_twosfx(const char * word, int len, int optflags, PfxEntry* ppfx, const FLAG needflag = NULL);
^
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT affixmgr.lo -MD -MP -MF .deps/affixmgr.Tpo -c affixmgr.cxx -o affixmgr.o >/dev/null 2>&1
mv -f .deps/affixmgr.Tpo .deps/affixmgr.Plo
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT csutil.lo -MD -MP -MF .deps/csutil.Tpo -c -o csutil.lo csutil.cxx
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT csutil.lo -MD -MP -MF .deps/csutil.Tpo -c csutil.cxx -DDLL_EXPORT -DPIC -o .libs/csutil.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT csutil.lo -MD -MP -MF .deps/csutil.Tpo -c csutil.cxx -o csutil.o >/dev/null 2>&1
mv -f .deps/csutil.Tpo .deps/csutil.Plo
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT dictmgr.lo -MD -MP -MF .deps/dictmgr.Tpo -c -o dictmgr.lo dictmgr.cxx
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT dictmgr.lo -MD -MP -MF .deps/dictmgr.Tpo -c dictmgr.cxx -DDLL_EXPORT -DPIC -o .libs/dictmgr.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT dictmgr.lo -MD -MP -MF .deps/dictmgr.Tpo -c dictmgr.cxx -o dictmgr.o >/dev/null 2>&1
mv -f .deps/dictmgr.Tpo .deps/dictmgr.Plo
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT hashmgr.lo -MD -MP -MF .deps/hashmgr.Tpo -c -o hashmgr.lo hashmgr.cxx
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT hashmgr.lo -MD -MP -MF .deps/hashmgr.Tpo -c hashmgr.cxx -DDLL_EXPORT -DPIC -o .libs/hashmgr.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT hashmgr.lo -MD -MP -MF .deps/hashmgr.Tpo -c hashmgr.cxx -o hashmgr.o >/dev/null 2>&1
mv -f .deps/hashmgr.Tpo .deps/hashmgr.Plo
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT hunspell.lo -MD -MP -MF .deps/hunspell.Tpo -c -o hunspell.lo hunspell.cxx
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT hunspell.lo -MD -MP -MF .deps/hunspell.Tpo -c hunspell.cxx -DDLL_EXPORT -DPIC -o .libs/hunspell.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT hunspell.lo -MD -MP -MF .deps/hunspell.Tpo -c hunspell.cxx -o hunspell.o >/dev/null 2>&1
mv -f .deps/hunspell.Tpo .deps/hunspell.Plo
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT suggestmgr.lo -MD -MP -MF .deps/suggestmgr.Tpo -c -o suggestmgr.lo suggestmgr.cxx
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT suggestmgr.lo -MD -MP -MF .deps/suggestmgr.Tpo -c suggestmgr.cxx -DDLL_EXPORT -DPIC -o .libs/suggestmgr.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT suggestmgr.lo -MD -MP -MF .deps/suggestmgr.Tpo -c suggestmgr.cxx -o suggestmgr.o >/dev/null 2>&1
mv -f .deps/suggestmgr.Tpo .deps/suggestmgr.Plo
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT phonet.lo -MD -MP -MF .deps/phonet.Tpo -c -o phonet.lo phonet.cxx
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT phonet.lo -MD -MP -MF .deps/phonet.Tpo -c phonet.cxx -DDLL_EXPORT -DPIC -o .libs/phonet.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT phonet.lo -MD -MP -MF .deps/phonet.Tpo -c phonet.cxx -o phonet.o >/dev/null 2>&1
mv -f .deps/phonet.Tpo .deps/phonet.Plo
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT filemgr.lo -MD -MP -MF .deps/filemgr.Tpo -c -o filemgr.lo filemgr.cxx
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT filemgr.lo -MD -MP -MF .deps/filemgr.Tpo -c filemgr.cxx -DDLL_EXPORT -DPIC -o .libs/filemgr.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT filemgr.lo -MD -MP -MF .deps/filemgr.Tpo -c filemgr.cxx -o filemgr.o >/dev/null 2>&1
mv -f .deps/filemgr.Tpo .deps/filemgr.Plo
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT hunzip.lo -MD -MP -MF .deps/hunzip.Tpo -c -o hunzip.lo hunzip.cxx
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT hunzip.lo -MD -MP -MF .deps/hunzip.Tpo -c hunzip.cxx -DDLL_EXPORT -DPIC -o .libs/hunzip.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT hunzip.lo -MD -MP -MF .deps/hunzip.Tpo -c hunzip.cxx -o hunzip.o >/dev/null 2>&1
mv -f .deps/hunzip.Tpo .deps/hunzip.Plo
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT replist.lo -MD -MP -MF .deps/replist.Tpo -c -o replist.lo replist.cxx
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT replist.lo -MD -MP -MF .deps/replist.Tpo -c replist.cxx -DDLL_EXPORT -DPIC -o .libs/replist.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -MT replist.lo -MD -MP -MF .deps/replist.Tpo -c replist.cxx -o replist.o >/dev/null 2>&1
mv -f .deps/replist.Tpo .deps/replist.Plo
/bin/sh ../../libtool --tag=CXX --mode=link g++ -fvisibility=hidden -DBUILDING_LIBHUNSPELL -g -O2 -no-undefined -o libhunspell-1.3.la -rpath /usr/local/lib affentry.lo affixmgr.lo csutil.lo dictmgr.lo hashmgr.lo hunspell.lo suggestmgr.lo phonet.lo filemgr.lo hunzip.lo replist.lo
libtool: link: rm -fr .libs/libhunspell-1.3.a .libs/libhunspell-1.3.dll.a .libs/libhunspell-1.3.la .libs/libhunspell-1.3.lai
libtool: link: g++ -shared -nostdlib /usr/lib/gcc/i686-pc-cygwin/4.8.3/crtbegin.o .libs/affentry.o .libs/affixmgr.o .libs/csutil.o .libs/dictmgr.o .libs/hashmgr.o .libs/hunspell.o .libs/suggestmgr.o .libs/phonet.o .libs/filemgr.o .libs/hunzip.o .libs/replist.o -L/usr/lib/gcc/i686-pc-cygwin/4.8.3 -L/usr/lib/gcc/i686-pc-cygwin/4.8.3/../../.. -lstdc++ -lgcc_s -lgcc -lcygwin -ladvapi32 -lshell32 -luser32 -lkernel32 -lgcc_s -lgcc /usr/lib/gcc/i686-pc-cygwin/4.8.3/crtend.o -o .libs/cyghunspell-1.3-0.dll -Wl,--enable-auto-image-base -Xlinker --out-implib -Xlinker .libs/libhunspell-1.3.dll.a
libtool: link: ar cru .libs/libhunspell-1.3.a affentry.o affixmgr.o csutil.o dictmgr.o hashmgr.o hunspell.o suggestmgr.o phonet.o filemgr.o hunzip.o replist.o
libtool: link: ranlib .libs/libhunspell-1.3.a
libtool: link: ( cd ".libs" && rm -f "libhunspell-1.3.la" && ln -s "../libhunspell-1.3.la" "libhunspell-1.3.la" )
make[3]: Leaving directory '/home/nuras/dene/hunspell-1.3.2/src/hunspell'
Making all in parsers
make[3]: Entering directory '/home/nuras/dene/hunspell-1.3.2/src/parsers'
g++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT firstparser.o -MD -MP -MF .deps/firstparser.Tpo -c -o firstparser.o firstparser.cxx
mv -f .deps/firstparser.Tpo .deps/firstparser.Po
g++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT htmlparser.o -MD -MP -MF .deps/htmlparser.Tpo -c -o htmlparser.o htmlparser.cxx
mv -f .deps/htmlparser.Tpo .deps/htmlparser.Po
g++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT latexparser.o -MD -MP -MF .deps/latexparser.Tpo -c -o latexparser.o latexparser.cxx
mv -f .deps/latexparser.Tpo .deps/latexparser.Po
g++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT manparser.o -MD -MP -MF .deps/manparser.Tpo -c -o manparser.o manparser.cxx
mv -f .deps/manparser.Tpo .deps/manparser.Po
g++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT textparser.o -MD -MP -MF .deps/textparser.Tpo -c -o textparser.o textparser.cxx
mv -f .deps/textparser.Tpo .deps/textparser.Po
rm -f libparsers.a
ar cru libparsers.a firstparser.o htmlparser.o latexparser.o manparser.o textparser.o
ranlib libparsers.a
/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -o testparser.exe firstparser.o htmlparser.o latexparser.o manparser.o testparser.o textparser.o ../hunspell/libhunspell-1.3.la
libtool: link: g++ -g -O2 -o .libs/testparser.exe firstparser.o htmlparser.o latexparser.o manparser.o testparser.o textparser.o ../hunspell/.libs/libhunspell-1.3.dll.a -L/usr/local/lib
make[3]: Leaving directory '/home/nuras/dene/hunspell-1.3.2/src/parsers'
Making all in tools
make[3]: Entering directory '/home/nuras/dene/hunspell-1.3.2/src/tools'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/hunspell -I../../src/parsers -g -O2 -MT analyze.o -MD -MP -MF .deps/analyze.Tpo -c -o analyze.o analyze.cxx
mv -f .deps/analyze.Tpo .deps/analyze.Po
/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -o analyze.exe analyze.o ../hunspell/libhunspell-1.3.la
libtool: link: g++ -g -O2 -o .libs/analyze.exe analyze.o ../hunspell/.libs/libhunspell-1.3.dll.a -L/usr/local/lib
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/hunspell -I../../src/parsers -g -O2 -MT chmorph.o -MD -MP -MF .deps/chmorph.Tpo -c -o chmorph.o chmorph.cxx
mv -f .deps/chmorph.Tpo .deps/chmorph.Po
/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -o chmorph.exe chmorph.o ../parsers/libparsers.a ../hunspell/libhunspell-1.3.la
libtool: link: g++ -g -O2 -o .libs/chmorph.exe chmorph.o ../parsers/libparsers.a ../hunspell/.libs/libhunspell-1.3.dll.a -L/usr/local/lib
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/hunspell -I../../src/parsers -g -O2 -MT hunspell.o -MD -MP -MF .deps/hunspell.Tpo -c -o hunspell.o hunspell.cxx
hunspell.cxx:119:21: fatal error: ncurses.h: No such file or directory
#include <ncurses.h>
^
compilation terminated.
Makefile:524: recipe for target 'hunspell.o' failed
make[3]: *** [hunspell.o] Error 1
make[3]: Leaving directory '/home/nuras/dene/hunspell-1.3.2/src/tools'
Makefile:329: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/nuras/dene/hunspell-1.3.2/src'
Makefile:425: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/nuras/dene/hunspell-1.3.2'
Makefile:330: recipe for target 'all' failed
make: *** [all] Error 2
I think I forgot the installing "readline package" I will try to install now.
if I succeed the compilation which directory will Cygwin put it the huspell's executables?
if anyone give me some help I will be appreciated. Thank you.
art
Expanding on my comment above, it does look like that you're missing libncursesw-devel. You can install that from the setup application that you used to install Cygwin.
I've downloaded the source for hunspell-1.3.2 and built it successfully on my machine.
I can now tell you that by default it installs into /usr/local.
Also, for better performance, you should add "--enable-shared=yes" to your configure command line options and add LDFLAGS="-no-undefined" to your options when you call "make". This will force the build scripts to build a shared library for libhunspell.
Finally, hunspell's configure script aborts almost immediately under 64-bit Cygwin, complaining that it can't recognize the system type. Since I notice that you're using 32-bit Cygwin, I did not do any research into how difficult this would be to correct. Fixing configure is probably pretty trivial, but that doesn't guarantee that hunspell will compile and run.
I was trying to follow this tutorial:
https://devcenter.heroku.com/articles/process-model
And in the very first step, I wget the file and run the ./configure script.
It complained about missing libevent-
➜ memcached-1.4.5 ./configure
checking build system type... i386-apple-darwin13.1.0
checking host system type... i386-apple-darwin13.1.0
checking target system type... i386-apple-darwin13.1.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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 for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for icc in use... no
checking for Sun cc in use... no
checking for gcc option to accept ISO C99... none needed
checking whether gcc and cc understand -c and -o together... yes
checking for a BSD-compatible install... /usr/bin/install -c
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 sasl/sasl.h usability... yes
checking sasl/sasl.h presence... yes
checking for sasl/sasl.h... yes
checking for gcov... /usr/bin/gcov
checking for main in -lgcov... no
checking for libevent directory... configure: error: libevent is required.
After that I did a
$ brew install libevent
Running the ./configure passed without any error:
➜ memcached-1.4.5 ./configure
checking build system type... i386-apple-darwin13.1.0
checking host system type... i386-apple-darwin13.1.0
checking target system type... i386-apple-darwin13.1.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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 for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for icc in use... no
checking for Sun cc in use... no
checking for gcc option to accept ISO C99... none needed
checking whether gcc and cc understand -c and -o together... yes
checking for a BSD-compatible install... /usr/bin/install -c
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 sasl/sasl.h usability... yes
checking sasl/sasl.h presence... yes
checking for sasl/sasl.h... yes
checking for gcov... /usr/bin/gcov
checking for main in -lgcov... no
checking for libevent directory... (system)
checking for library containing socket... none required
checking for library containing gethostbyname... none required
checking for library containing umem_cache_create... no
checking for library containing gethugepagesizes... no
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inttypes.h... (cached) yes
checking for print macros for integers (C99 section 7.8.1)... yes
checking for an ANSI C-conforming const... yes
checking for socklen_t... yes
checking for endianness... little
checking for htonll... no
checking for library containing pthread_create... none required
checking for mlockall... yes
checking for getpagesizes... no
checking for memcntl... no
checking for sigignore... yes
checking for alignment... need
checking for setppriv... no
checking umem.h usability... no
checking umem.h presence... no
checking for umem.h... no
checking for xml2rfc... no
checking for xsltproc... /usr/bin/xsltproc
configure: creating ./config.status
config.status: creating Makefile
config.status: creating doc/Makefile
config.status: creating config.h
config.status: executing depfiles commands
then,
➜ memcached-1.4.5 make
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive
Making all in doc
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-am
make[3]: Nothing to be done for `all-am'.
gcc -DHAVE_CONFIG_H -I. -DNDEBUG -g -O2 -pthread -Wall -Werror -pedantic -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -MT memcached-memcached.o -MD -MP -MF .deps/memcached-memcached.Tpo -c -o memcached-memcached.o `test -f 'memcached.c' || echo './'`memcached.c
mv -f .deps/memcached-memcached.Tpo .deps/memcached-memcached.Po
gcc -DHAVE_CONFIG_H -I. -DNDEBUG -g -O2 -pthread -Wall -Werror -pedantic -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -MT memcached-hash.o -MD -MP -MF .deps/memcached-hash.Tpo -c -o memcached-hash.o `test -f 'hash.c' || echo './'`hash.c
mv -f .deps/memcached-hash.Tpo .deps/memcached-hash.Po
gcc -DHAVE_CONFIG_H -I. -DNDEBUG -g -O2 -pthread -Wall -Werror -pedantic -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -MT memcached-slabs.o -MD -MP -MF .deps/memcached-slabs.Tpo -c -o memcached-slabs.o `test -f 'slabs.c' || echo './'`slabs.c
mv -f .deps/memcached-slabs.Tpo .deps/memcached-slabs.Po
gcc -DHAVE_CONFIG_H -I. -DNDEBUG -g -O2 -pthread -Wall -Werror -pedantic -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -MT memcached-items.o -MD -MP -MF .deps/memcached-items.Tpo -c -o memcached-items.o `test -f 'items.c' || echo './'`items.c
mv -f .deps/memcached-items.Tpo .deps/memcached-items.Po
gcc -DHAVE_CONFIG_H -I. -DNDEBUG -g -O2 -pthread -Wall -Werror -pedantic -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -MT memcached-assoc.o -MD -MP -MF .deps/memcached-assoc.Tpo -c -o memcached-assoc.o `test -f 'assoc.c' || echo './'`assoc.c
mv -f .deps/memcached-assoc.Tpo .deps/memcached-assoc.Po
gcc -DHAVE_CONFIG_H -I. -DNDEBUG -g -O2 -pthread -Wall -Werror -pedantic -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -MT memcached-thread.o -MD -MP -MF .deps/memcached-thread.Tpo -c -o memcached-thread.o `test -f 'thread.c' || echo './'`thread.c
mv -f .deps/memcached-thread.Tpo .deps/memcached-thread.Po
gcc -DHAVE_CONFIG_H -I. -DNDEBUG -g -O2 -pthread -Wall -Werror -pedantic -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -MT memcached-daemon.o -MD -MP -MF .deps/memcached-daemon.Tpo -c -o memcached-daemon.o `test -f 'daemon.c' || echo './'`daemon.c
mv -f .deps/memcached-daemon.Tpo .deps/memcached-daemon.Po
gcc -DHAVE_CONFIG_H -I. -DNDEBUG -g -O2 -pthread -Wall -Werror -pedantic -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -MT memcached-stats.o -MD -MP -MF .deps/memcached-stats.Tpo -c -o memcached-stats.o `test -f 'stats.c' || echo './'`stats.c
mv -f .deps/memcached-stats.Tpo .deps/memcached-stats.Po
gcc -DHAVE_CONFIG_H -I. -DNDEBUG -g -O2 -pthread -Wall -Werror -pedantic -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -MT memcached-util.o -MD -MP -MF .deps/memcached-util.Tpo -c -o memcached-util.o `test -f 'util.c' || echo './'`util.c
mv -f .deps/memcached-util.Tpo .deps/memcached-util.Po
gcc -DHAVE_CONFIG_H -I. -DNDEBUG -g -O2 -pthread -Wall -Werror -pedantic -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -MT memcached-cache.o -MD -MP -MF .deps/memcached-cache.Tpo -c -o memcached-cache.o `test -f 'cache.c' || echo './'`cache.c
mv -f .deps/memcached-cache.Tpo .deps/memcached-cache.Po
gcc -g -O2 -pthread -Wall -Werror -pedantic -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -o memcached memcached-memcached.o memcached-hash.o memcached-slabs.o memcached-items.o memcached-assoc.o memcached-thread.o memcached-daemon.o memcached-stats.o memcached-util.o memcached-cache.o -levent
clang: error: argument unused during compilation: '-pthread'
make[2]: *** [memcached] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
Ends up with this error. I haven't ever build anything from source till now so some pointers in how to go about debugging this kind of problem will be helpful. Looking at another post I see the following info maybe helpful:
➜ memcached-1.4.5 gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
Target: x86_64-apple-darwin13.1.0
Thread model: posix
And my os is mac os x 10.9.2
Thanks and regards,
Dhruv Kapur.