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