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Hi, I am having trouble installing Arachne from the broad institute. (http://www.broadinstitute.org/crd/wi...chne_Main_Page)
When I use the ./configure command, I do not get any obvious errors. However, the make command always fails. (I'm using ubuntu through Oracle's VirtualBox.)
Here is my output for the .configure command and for the make step:
kristen@kristen-VirtualBox:~/Desktop/arachne-40459$ ./configure --with-xerces=xerces-c-3.1.1
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for 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 for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
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 ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether byte ordering is bigendian... no
g++ version is >= 4.3.3... yes
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for gcc option to support OpenMP... -fopenmp
checking validity of OpenMP configuation.... checking for Xerces C++ Parser headers in xerces-c-3.1.1/include and xerces-c-3.1.1/include/xercesc... found
checking for Xerces C++ Parser libraries... found
checking for Xerces C++ Parser... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/config.h
config.status: src/config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
kristen@kristen-VirtualBox:~/Desktop/arachne-40459$ make
Making all in src
make[1]: Entering directory `/home/kristen/Desktop/arachne-40459/src'
make all-am
make[2]: Entering directory `/home/kristen/Desktop/arachne-40459/src'
g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=3.0.0-15-generic -DMAKE_RELEASE=3.0 -DSVN_VERSION=40459 -Ixerces-c-3.1.1/include -Ixerces-c-3.1.1/include/xercesc -fopenmp -g -O2 -Wextra -Wall -ansi -pedantic -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -ftemplate-depth-50 -mieee-fp -fno-strict-aliasing -iquote . -ggdb3 -DNDEBUG -MT Combinatorics.o -MD -MP -MF .deps/Combinatorics.Tpo -c -o Combinatorics.o `test -f 'math/Combinatorics.cc' || echo './'`math/Combinatorics.cc
In file included from ./feudal/MasterVec.h:24:0,
from ./VecString.h:14,
from ./CoreTools.h:22,
from math/Combinatorics.cc:11:
./feudal/OuterVec.h: In member function ‘OuterVec<T, S, A>::size_type OuterVec<T, S, A>::max_size() const’:
./feudal/OuterVec.h:205:21: warning: left shift count >= width of type [enabled by default]
In file included from ./feudal/FeudalString.h:23:0,
from ./feudal/CharString.h:19,
from ./String.h:13,
from ./system/System.h:17,
from ./CoreTools.h:17,
from math/Combinatorics.cc:11:
./feudal/SmallVec.h: In member function ‘SmallVec<T, A>& SmallVec<T, A>:
ush_back(const T&, float, SmallVec<T, A>::size_type) [with T = char, A = MempoolAllocator<char>, SmallVec<T, A> = SmallVec<char, MempoolAllocator<char> >, SmallVec<T, A>::size_type = unsigned int]’:
./feudal/SmallVec.h:226:36: instantiated from ‘SmallVec<T, A>& SmallVec<T, A>:ush_back(const T&) [with T = char, A = MempoolAllocator<char>, SmallVec<T, A> = SmallVec<char, MempoolAllocator<char> >]’
./feudal/FeudalString.h:175:7: instantiated from ‘FeudalString<charT, Traits>& FeudalString<charT, Traits>:ush_back(FeudalString<charT, Traits>::value_type) [with charT = char, Traits = std::char_traits<char>, FeudalString<charT, Traits> = FeudalString<char, std::char_traits<char> >, FeudalString<charT, Traits>::value_type = char]’
./feudal/CharString.h:148:20: instantiated from here
./feudal/SmallVec.h:237:9: error: no matching function for call to ‘max(long unsigned int, const unsigned int&)’
./feudal/SmallVec.h:237:9: note: candidates are:
/usr/include/c++/4.6/bits/stl_algobase.h:210:5: note: template<class _Tp> const _Tp& std::max(const _Tp&, const _Tp&)
/usr/include/c++/4.6/bits/stl_algobase.h:254:5: note: template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare)
make[2]: *** [Combinatorics.o] Error 1
make[2]: Leaving directory `/home/kristen/Desktop/arachne-40459/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/kristen/Desktop/arachne-40459/src'
make: *** [all-recursive] Error 1
kristen@kristen-VirtualBox:~/Desktop/arachne-40459$
I also looked in config.log file, and I think this part might be the problem:
configure:3346: $? = 0
configure:3335: gcc -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/4.6.1/lto-wrapper
Target: i686-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 4.6.1-9ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++,go --prefix=/usr --program-suffix=-4.6 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-plugin --enable-objc-gc --enable-targets=all --disable-werror --with-arch-32=i686 --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu
Thread model: posix
gcc version 4.6.1 (Ubuntu/Linaro 4.6.1-9ubuntu3)
configure:3346: $? = 0
configure:3335: gcc -V >&5
gcc: error: unrecognized option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:3346: $? = 4
configure:3335: gcc -qversion >&5
gcc: error: unrecognized option '-qversion'
gcc: fatal error: no input files
compilation terminated.
I found this thread:
old.nabble.com/cannot-compile-arrrghh...-td32746084.html
which seemed to have a similar error message, and so it may be a problem with gmp, mpfr, and mpc as suggested. (I tried to install each of these components before making the symbolic links, but I'm now getting "configure: error: libgmp not found or uses a different ABI (including static vs shared)" when I try to install mpfr. I think I have gmp-5.0.3 successfully installed and the symbolic link created, but just fixing gmp wasn't enough to resolve the error in the arachne config log.)
So what should I do? Is there an easier way to resolve my arachne config error? If the error really is due to problems with gmp/mpfr/mpc, is there a version of gcc I can download with these components already included? I am not very experienced with unix/bioinformatics so I am having a lot of problems trouble shooting.
Thanks for your help!
When I use the ./configure command, I do not get any obvious errors. However, the make command always fails. (I'm using ubuntu through Oracle's VirtualBox.)
Here is my output for the .configure command and for the make step:
kristen@kristen-VirtualBox:~/Desktop/arachne-40459$ ./configure --with-xerces=xerces-c-3.1.1
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for 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 for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
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 ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether byte ordering is bigendian... no
g++ version is >= 4.3.3... yes
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for gcc option to support OpenMP... -fopenmp
checking validity of OpenMP configuation.... checking for Xerces C++ Parser headers in xerces-c-3.1.1/include and xerces-c-3.1.1/include/xercesc... found
checking for Xerces C++ Parser libraries... found
checking for Xerces C++ Parser... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/config.h
config.status: src/config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
kristen@kristen-VirtualBox:~/Desktop/arachne-40459$ make
Making all in src
make[1]: Entering directory `/home/kristen/Desktop/arachne-40459/src'
make all-am
make[2]: Entering directory `/home/kristen/Desktop/arachne-40459/src'
g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=3.0.0-15-generic -DMAKE_RELEASE=3.0 -DSVN_VERSION=40459 -Ixerces-c-3.1.1/include -Ixerces-c-3.1.1/include/xercesc -fopenmp -g -O2 -Wextra -Wall -ansi -pedantic -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -ftemplate-depth-50 -mieee-fp -fno-strict-aliasing -iquote . -ggdb3 -DNDEBUG -MT Combinatorics.o -MD -MP -MF .deps/Combinatorics.Tpo -c -o Combinatorics.o `test -f 'math/Combinatorics.cc' || echo './'`math/Combinatorics.cc
In file included from ./feudal/MasterVec.h:24:0,
from ./VecString.h:14,
from ./CoreTools.h:22,
from math/Combinatorics.cc:11:
./feudal/OuterVec.h: In member function ‘OuterVec<T, S, A>::size_type OuterVec<T, S, A>::max_size() const’:
./feudal/OuterVec.h:205:21: warning: left shift count >= width of type [enabled by default]
In file included from ./feudal/FeudalString.h:23:0,
from ./feudal/CharString.h:19,
from ./String.h:13,
from ./system/System.h:17,
from ./CoreTools.h:17,
from math/Combinatorics.cc:11:
./feudal/SmallVec.h: In member function ‘SmallVec<T, A>& SmallVec<T, A>:
ush_back(const T&, float, SmallVec<T, A>::size_type) [with T = char, A = MempoolAllocator<char>, SmallVec<T, A> = SmallVec<char, MempoolAllocator<char> >, SmallVec<T, A>::size_type = unsigned int]’:./feudal/SmallVec.h:226:36: instantiated from ‘SmallVec<T, A>& SmallVec<T, A>:
ush_back(const T&) [with T = char, A = MempoolAllocator<char>, SmallVec<T, A> = SmallVec<char, MempoolAllocator<char> >]’./feudal/FeudalString.h:175:7: instantiated from ‘FeudalString<charT, Traits>& FeudalString<charT, Traits>:
ush_back(FeudalString<charT, Traits>::value_type) [with charT = char, Traits = std::char_traits<char>, FeudalString<charT, Traits> = FeudalString<char, std::char_traits<char> >, FeudalString<charT, Traits>::value_type = char]’./feudal/CharString.h:148:20: instantiated from here
./feudal/SmallVec.h:237:9: error: no matching function for call to ‘max(long unsigned int, const unsigned int&)’
./feudal/SmallVec.h:237:9: note: candidates are:
/usr/include/c++/4.6/bits/stl_algobase.h:210:5: note: template<class _Tp> const _Tp& std::max(const _Tp&, const _Tp&)
/usr/include/c++/4.6/bits/stl_algobase.h:254:5: note: template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare)
make[2]: *** [Combinatorics.o] Error 1
make[2]: Leaving directory `/home/kristen/Desktop/arachne-40459/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/kristen/Desktop/arachne-40459/src'
make: *** [all-recursive] Error 1
kristen@kristen-VirtualBox:~/Desktop/arachne-40459$
I also looked in config.log file, and I think this part might be the problem:
configure:3346: $? = 0
configure:3335: gcc -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/4.6.1/lto-wrapper
Target: i686-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 4.6.1-9ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++,go --prefix=/usr --program-suffix=-4.6 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-plugin --enable-objc-gc --enable-targets=all --disable-werror --with-arch-32=i686 --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu
Thread model: posix
gcc version 4.6.1 (Ubuntu/Linaro 4.6.1-9ubuntu3)
configure:3346: $? = 0
configure:3335: gcc -V >&5
gcc: error: unrecognized option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:3346: $? = 4
configure:3335: gcc -qversion >&5
gcc: error: unrecognized option '-qversion'
gcc: fatal error: no input files
compilation terminated.
I found this thread:
old.nabble.com/cannot-compile-arrrghh...-td32746084.html
which seemed to have a similar error message, and so it may be a problem with gmp, mpfr, and mpc as suggested. (I tried to install each of these components before making the symbolic links, but I'm now getting "configure: error: libgmp not found or uses a different ABI (including static vs shared)" when I try to install mpfr. I think I have gmp-5.0.3 successfully installed and the symbolic link created, but just fixing gmp wasn't enough to resolve the error in the arachne config log.)
So what should I do? Is there an easier way to resolve my arachne config error? If the error really is due to problems with gmp/mpfr/mpc, is there a version of gcc I can download with these components already included? I am not very experienced with unix/bioinformatics so I am having a lot of problems trouble shooting.
Thanks for your help!