numpy not found when run ./configure
when I run ./configure this is the output I get: checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking how to create a pax tar archive... gnutar checking whether make supports nested variables... (cached) yes checking whether make supports the include directive... yes (GNU style) 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for library containing strerror... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for wchar.h... yes checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... gcc3 checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking whether g++ supports C++17 features by default... no checking whether g++ supports C++17 features with -std=gnu++17... yes configure: WARNING: C++17 is not yet standardized, so the checks may change in incompatible ways anytime checking whether to enable debug info... no checking whether to enable parallel algorithms with openmp... checking for OpenMP flag of C++ compiler... -fopenmp checking whether to enable cairo drawing... yes checking for EXPAT... yes checking for a Python interpreter with version >= 2.7... python checking for python... /usr/bin/python checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/dist-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages checking for python2.7... (cached) /usr/bin/python checking for a version of Python >= '2.1.0'... yes checking for a version of Python == '2.7.17'... yes checking for the distutils Python package... yes checking for Python include path... -I/usr/include/python2.7 checking for Python library path... -L/usr/lib -lpython2.7 checking for Python site-packages path... /usr/lib/python2.7/dist-packages checking python extra libraries... -lpthread -ldl -lutil -lm checking python extra linking flags... -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions checking consistency of all components of python development environment... yes checking for boostlib >= 1.55.0 (105500)... yes checking whether the Boost::Python library is available... yes checking whether boost_python27 is the correct library... no checking whether boost_python-py27 is the correct library... yes checking whether the Boost::IOStreams library is available... yes checking for exit in -lboost_iostreams... yes checking whether the Boost::Regex library is available... yes checking for exit in -lboost_regex... yes checking whether the Boost::Context library is available... yes checking for exit in -lboost_context... yes checking whether the Boost::Coroutine library is available... yes checking for exit in -lboost_coroutine... yes checking whether the Boost::Graph library is available... yes checking for exit in -lboost_graph... yes checking whether the Boost::Thread library is available... yes checking for exit in -lboost_thread... yes checking for __gmpz_init in -lgmp... yes checking for __gmpz_init in -lgmp... (cached) yes checking whether CGAL is available in /usr... yes checking whether to enable debbuging with valgrind... no checking python module: numpy... no configure: error: failed to find required module numpy I have numpy istalled in the right place (Ibelieve) To check this I've run : pip install numpy and got: numpy in /home/kaspersegers/.local/lib/python3.6/site-packages (1.17.3) What can I do to remedy this? -- Sent from: https://nabble.skewed.de/
Ni! Your check says you've got numpy installed for python3.6 ... and yet your configure output tells us you're compiling for python-2.7. Which version of graph-tool are you even compiling ? Recent versions require python 3. Old versions are not supported and not recommended. Also, make sure you have a very good reason to be compiling it instead of using one of the many prepackaged options <https://git.skewed.de/count0/graph-tool/-/wikis/installation-instructions>. Cheers, .~´ On Wed, Apr 7, 2021 at 12:25 PM Kasper <kasperandus@gmail.com> wrote:
when I run ./configure this is the output I get:
checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking how to create a pax tar archive... gnutar checking whether make supports nested variables... (cached) yes checking whether make supports the include directive... yes (GNU style) 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for library containing strerror... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for wchar.h... yes checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... gcc3 checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking whether g++ supports C++17 features by default... no checking whether g++ supports C++17 features with -std=gnu++17... yes configure: WARNING: C++17 is not yet standardized, so the checks may change in incompatible ways anytime checking whether to enable debug info... no checking whether to enable parallel algorithms with openmp... checking for OpenMP flag of C++ compiler... -fopenmp checking whether to enable cairo drawing... yes checking for EXPAT... yes checking for a Python interpreter with version >= 2.7... python checking for python... /usr/bin/python checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/dist-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages checking for python2.7... (cached) /usr/bin/python checking for a version of Python >= '2.1.0'... yes checking for a version of Python == '2.7.17'... yes checking for the distutils Python package... yes checking for Python include path... -I/usr/include/python2.7 checking for Python library path... -L/usr/lib -lpython2.7 checking for Python site-packages path... /usr/lib/python2.7/dist-packages checking python extra libraries... -lpthread -ldl -lutil -lm checking python extra linking flags... -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions checking consistency of all components of python development environment... yes checking for boostlib >= 1.55.0 (105500)... yes checking whether the Boost::Python library is available... yes checking whether boost_python27 is the correct library... no checking whether boost_python-py27 is the correct library... yes checking whether the Boost::IOStreams library is available... yes checking for exit in -lboost_iostreams... yes checking whether the Boost::Regex library is available... yes checking for exit in -lboost_regex... yes checking whether the Boost::Context library is available... yes checking for exit in -lboost_context... yes checking whether the Boost::Coroutine library is available... yes checking for exit in -lboost_coroutine... yes checking whether the Boost::Graph library is available... yes checking for exit in -lboost_graph... yes checking whether the Boost::Thread library is available... yes checking for exit in -lboost_thread... yes checking for __gmpz_init in -lgmp... yes checking for __gmpz_init in -lgmp... (cached) yes checking whether CGAL is available in /usr... yes checking whether to enable debbuging with valgrind... no checking python module: numpy... no configure: error: failed to find required module numpy
I have numpy istalled in the right place (Ibelieve) To check this I've run : pip install numpy and got: numpy in /home/kaspersegers/.local/lib/python3.6/site-packages (1.17.3)
What can I do to remedy this?
-- Sent from: https://nabble.skewed.de/ _______________________________________________ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
Thanks for your reply I'm trying to install graph-tool-2.37 is that an older version ? I thougth it was a newer one so python3 should be all right no? -- Sent from: https://nabble.skewed.de/
Thanks for your reply! I'm trying to install graph-tool-2.37 which I believed to be a newer version, so Python3 should be all right or am I wrong? cheers Kasper -- Sent from: https://nabble.skewed.de/
Ni! Hi, That is the good version. It seems the configure script wasn't updated to require python3 until later. I'm going to stress this again: please, first try using a prepackaged build. Only in case none of the prepackaged options serve you, then: 0. Make sure you've read and understood the the Manual compilation instructions <https://git.skewed.de/count0/graph-tool/-/wikis/installation-instructions#manual-compilation> . 1. You must tell configure to use the right version of python by calling it with `PYTHON=python3 ./configure`. In this way it will hopefully detect the right python version. 2. If that doesn't help, try checking out and compiling the `master` branch from git. Configure should make all the right checks in that (when using git branches you'll have to first generate `configure` yourself by running `./autogen.sh`). If you don't know git and still want to try this, there are plenty of tutorials online. If you need to ask more questions, describe in detail the system you're compiling in (distribution, version, how was python3 installed etc), and dump the whole of config.log into some pastebin-like URL. Otherwise we won't be able to help. Best, .~´ On Wed, Apr 7, 2021 at 12:39 PM Kasper <kasperandus@gmail.com> wrote:
Thanks for your reply!
I'm trying to install graph-tool-2.37 which I believed to be a newer version, so Python3 should be all right or am I wrong?
cheers Kasper
-- Sent from: https://nabble.skewed.de/ _______________________________________________ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
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