Scenario: building sage 8.6 from source. Build seems to want to make scipy-1.1.0. Final results were: Error building Sage.
The following package(s) may have failed to build (not necessarily during this run of 'make all-start'): * package: scipy-1.1.0 log file: /usr/local/src/Misc/sage-8.6/logs/pkgs/scipy-1.1.0.log build directory: /usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0 The build directory may contain configuration files and other potentially helpful information. WARNING: if you now run 'make' again, the build directory will, by default, be deleted. Set the environment variable SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this. make[1]: *** [all-start] Error 1 make[1]: Leaving directory `/usr/local/src/Misc/sage-8.6' make: *** [all] Error 2 Examine log file and notice: Original error was: libgfortran.so.3: cannot open shared object file: No such file or directory But examination to find this shows >>> *locate libgfortran.so.* /usr/lib/libgfortran.so.5 /usr/lib/libgfortran.so.5.0.0 /usr/lib/gcc/x86_64-pc-linux-gnu/5.5.0/libgfortran.so.3 /usr/lib/gcc/x86_64-pc-linux-gnu/5.5.0/libgfortran.so.3.0.0 /usr/lib/gcc/x86_64-pc-linux-gnu/6.4.1/libgfortran.so.3 /usr/lib/gcc/x86_64-pc-linux-gnu/6.4.1/libgfortran.so.3.0.0 /usr/lib32/libgfortran.so.5 /usr/lib32/libgfortran.so.5.0.0 Trying subshell method: /usr/local/src/Misc/sage-8.6> (*cd '/usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0' && '/usr/local/src/Misc/sage-8.6/sage' --sh)* Starting subshell with Sage environment variables set. Don't forget to exit when you are done. Beware: * Do not do anything with other copies of Sage on your system. * Do not use this for installing Sage packages using "sage -i" or for running "make" at Sage's root directory. These should be done outside the Sage shell. Bypassing shell configuration files... Note: SAGE_ROOT=/usr/local/src/Misc/sage-8.6 (sage-sh) isaac@Light1DAW:scipy-1.1.0$ *pip install scipy* Collecting scipy Downloading https://files.pythonhosted.org/packages/45/d1/7c2b33a5daee3d67752d043fe7e1476c4465788b0b6e59367fd71fdf684a/scipy-1.2.0-cp27-cp27mu-manylinux1_x86_64.whl (26.6MB) ... Requirement already satisfied: numpy>=1.8.2 in /usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages (from scipy) (1.15.4) Installing collected packages: scipy Successfully installed scipy-1.2.0 (sage-sh) isaac@Light1DAW:scipy-1.1.0$ *exit* exit It hints that numpy needs reinstalling ** inside the install shell ** . I am at a loss as to how to proceed. I will attach the log file. Please help? Consider that I am a sysadmin but lost. -- You received this message because you are subscribed to the Google Groups "sage-support" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/sage-support. For more options, visit https://groups.google.com/d/optout.
Found local metadata for scipy-1.1.0 Using cached file /usr/local/src/Misc/sage-8.6/upstream/scipy-1.1.0.tar.gz scipy-1.1.0 ==================================================== Setting up build directory for scipy-1.1.0 Finished extraction No patch files found in ../patches **************************************************** Host system: Linux Light1DAW 4.20.3-arch1-1-ARCH #1 SMP PREEMPT Wed Jan 16 22:38:58 UTC 2019 x86_64 GNU/Linux **************************************************** C compiler: gcc C compiler version: Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.1/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /build/gcc/src/gcc/configure --prefix=/usr --libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=https://bugs.archlinux.org/ --enable-languages=c,c++,ada,fortran,go,lto,objc,obj-c++ --enable-shared --enable-threads=posix --enable-libmpx --with-system-zlib --with-isl --enable-__cxa_atexit --disable-libunwind-exceptions --enable-clocale=gnu --disable-libstdcxx-pch --disable-libssp --enable-gnu-unique-object --enable-linker-build-id --enable-lto --enable-plugin --enable-install-libiberty --with-linker-hash-style=gnu --enable-gnu-indirect-function --enable-multilib --disable-werror --enable-checking=release --enable-default-pie --enable-default-ssp --enable-cet=auto Thread model: posix gcc version 8.2.1 20181127 (GCC) **************************************************** No record that 'scipy' was ever installed; skipping uninstall Note: CFLAGS, CXXFLAGS and SHAREDFLAGS are taken from distutils, so their current settings are ignored. Installing scipy-1.1.0 Installing package scipy using pip2 Ignoring indexes: https://pypi.org/simple Created temporary directory: /tmp/pip-ephem-wheel-cache-Tg1Dyx Created temporary directory: /tmp/pip-req-tracker-BYAA2d Created requirements tracker '/tmp/pip-req-tracker-BYAA2d' Created temporary directory: /tmp/pip-install-DQAnRR Processing /usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0/src Created temporary directory: /tmp/pip-req-build-oy1fYY Added file:///usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0/src to build tracker '/tmp/pip-req-tracker-BYAA2d' Running setup.py (path:/tmp/pip-req-build-oy1fYY/setup.py) egg_info for package from file:///usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0/src Running command python setup.py egg_info running egg_info creating pip-egg-info/scipy.egg-info writing requirements to pip-egg-info/scipy.egg-info/requires.txt writing pip-egg-info/scipy.egg-info/PKG-INFO writing top-level names to pip-egg-info/scipy.egg-info/top_level.txt writing dependency_links to pip-egg-info/scipy.egg-info/dependency_links.txt writing manifest file 'pip-egg-info/scipy.egg-info/SOURCES.txt' reading manifest file 'pip-egg-info/scipy.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*_subr_*.f' found under directory 'scipy/linalg/src/id_dist/src' no previously-included directories found matching 'benchmarks/env' no previously-included directories found matching 'benchmarks/results' no previously-included directories found matching 'benchmarks/html' no previously-included directories found matching 'benchmarks/scipy' no previously-included directories found matching 'scipy/special/tests/data/boost' no previously-included directories found matching 'scipy/special/tests/data/gsl' no previously-included directories found matching 'scipy/special/tests/data/local' no previously-included directories found matching 'doc/build' no previously-included directories found matching 'doc/source/generated' no previously-included directories found matching '*/__pycache__' warning: no previously-included files matching '*~' found anywhere in distribution warning: no previously-included files matching '*.bak' found anywhere in distribution warning: no previously-included files matching '*.swp' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution writing manifest file 'pip-egg-info/scipy.egg-info/SOURCES.txt' Source in /tmp/pip-req-build-oy1fYY has version 1.1.0, which satisfies requirement scipy==1.1.0 from file:///usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0/src Removed scipy==1.1.0 from file:///usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0/src from build tracker '/tmp/pip-req-tracker-BYAA2d' Installing collected packages: scipy Created temporary directory: /tmp/pip-record-dPzF3g Running setup.py install for scipy: started Running command /usr/local/src/Misc/sage-8.6/local/bin/python2 -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-oy1fYY/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" --no-user-cfg install --record /tmp/pip-record-dPzF3g/install-record.txt --single-version-externally-managed --root /usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0/inst --compile Note: if you need reliable uninstall behavior, then install with pip instead of using `setup.py install`: - `pip install .` (from a git repo or downloaded source release) - `pip install scipy` (last SciPy release on PyPI) Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-req-build-oy1fYY/setup.py", line 474, in <module> setup_package() File "/tmp/pip-req-build-oy1fYY/setup.py", line 450, in setup_package from numpy.distutils.core import setup File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/numpy/__init__.py", line 142, in <module> from . import add_newdocs File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module> from numpy.lib import add_newdoc File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8, in <module> from .type_check import * File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in <module> import numpy.core.numeric as _nx File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/numpy/core/__init__.py", line 26, in <module> raise ImportError(msg) ImportError: Importing the multiarray numpy extension module failed. Most likely you are trying to import a failed build of numpy. If you're working with a numpy git repo, try `git clean -xdf` (removes all files not under version control). Otherwise reinstall numpy. Original error was: libgfortran.so.3: cannot open shared object file: No such file or directory Running setup.py install for scipy: finished with status 'error' Cleaning up... Removing source in /tmp/pip-req-build-oy1fYY Removed build tracker '/tmp/pip-req-tracker-BYAA2d' Command "/usr/local/src/Misc/sage-8.6/local/bin/python2 -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-oy1fYY/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" --no-user-cfg install --record /tmp/pip-record-dPzF3g/install-record.txt --single-version-externally-managed --root /usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0/inst --compile" failed with error code 1 in /tmp/pip-req-build-oy1fYY/ Exception information: Traceback (most recent call last): File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/pip/_internal/basecommand.py", line 141, in main status = self.run(options, args) File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/pip/_internal/commands/install.py", line 347, in run use_user_site=options.use_user_site, File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/pip/_internal/req/__init__.py", line 49, in install_given_reqs **kwargs File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/pip/_internal/req/req_install.py", line 972, in install spinner=spinner, File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/pip/_internal/utils/misc.py", line 701, in call_subprocess % (command_desc, proc.returncode, cwd)) InstallationError: Command "/usr/local/src/Misc/sage-8.6/local/bin/python2 -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-oy1fYY/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" --no-user-cfg install --record /tmp/pip-record-dPzF3g/install-record.txt --single-version-externally-managed --root /usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0/inst --compile" failed with error code 1 in /tmp/pip-req-build-oy1fYY/ Error: installing with pip2 failed ******************************************************************************** Error installing scipy-1.1.0 ******************************************************************************** real 0m6.693s user 0m4.980s sys 0m1.178s ************************************************************************ Error installing package scipy-1.1.0 ************************************************************************ Please email sage-devel (http://groups.google.com/group/sage-devel) explaining the problem and including the log file /usr/local/src/Misc/sage-8.6/logs/pkgs/scipy-1.1.0.log Describe your computer, operating system, etc. If you want to try to fix the problem yourself, *don't* just cd to /usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0 and type 'make' or whatever is appropriate. Instead, the following commands setup all environment variables correctly and load a subshell for you to debug the error: (cd '/usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0' && '/usr/local/src/Misc/sage-8.6/sage' --sh) When you are done debugging, you can type "exit" to leave the subshell. ************************************************************************ Found local metadata for scipy-1.1.0 Using cached file /usr/local/src/Misc/sage-8.6/upstream/scipy-1.1.0.tar.gz scipy-1.1.0 ==================================================== Moving old directory scipy-1.1.0 to /usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/old... Setting up build directory for scipy-1.1.0 Finished extraction No patch files found in ../patches **************************************************** Host system: Linux Light1DAW 4.20.3-arch1-1-ARCH #1 SMP PREEMPT Wed Jan 16 22:38:58 UTC 2019 x86_64 GNU/Linux **************************************************** C compiler: gcc C compiler version: Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.1/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /build/gcc/src/gcc/configure --prefix=/usr --libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=https://bugs.archlinux.org/ --enable-languages=c,c++,ada,fortran,go,lto,objc,obj-c++ --enable-shared --enable-threads=posix --enable-libmpx --with-system-zlib --with-isl --enable-__cxa_atexit --disable-libunwind-exceptions --enable-clocale=gnu --disable-libstdcxx-pch --disable-libssp --enable-gnu-unique-object --enable-linker-build-id --enable-lto --enable-plugin --enable-install-libiberty --with-linker-hash-style=gnu --enable-gnu-indirect-function --enable-multilib --disable-werror --enable-checking=release --enable-default-pie --enable-default-ssp --enable-cet=auto Thread model: posix gcc version 8.2.1 20181127 (GCC) **************************************************** No record that 'scipy' was ever installed; skipping uninstall Note: CFLAGS, CXXFLAGS and SHAREDFLAGS are taken from distutils, so their current settings are ignored. Installing scipy-1.1.0 Installing package scipy using pip2 Ignoring indexes: https://pypi.org/simple Created temporary directory: /tmp/pip-ephem-wheel-cache-yQwTzp Created temporary directory: /tmp/pip-req-tracker-SwH_RJ Created requirements tracker '/tmp/pip-req-tracker-SwH_RJ' Created temporary directory: /tmp/pip-install-yVo2MZ Processing /usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0/src Created temporary directory: /tmp/pip-req-build-wvhwk4 Added file:///usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0/src to build tracker '/tmp/pip-req-tracker-SwH_RJ' Running setup.py (path:/tmp/pip-req-build-wvhwk4/setup.py) egg_info for package from file:///usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0/src Running command python setup.py egg_info running egg_info creating pip-egg-info/scipy.egg-info writing requirements to pip-egg-info/scipy.egg-info/requires.txt writing pip-egg-info/scipy.egg-info/PKG-INFO writing top-level names to pip-egg-info/scipy.egg-info/top_level.txt writing dependency_links to pip-egg-info/scipy.egg-info/dependency_links.txt writing manifest file 'pip-egg-info/scipy.egg-info/SOURCES.txt' reading manifest file 'pip-egg-info/scipy.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*_subr_*.f' found under directory 'scipy/linalg/src/id_dist/src' no previously-included directories found matching 'benchmarks/env' no previously-included directories found matching 'benchmarks/results' no previously-included directories found matching 'benchmarks/html' no previously-included directories found matching 'benchmarks/scipy' no previously-included directories found matching 'scipy/special/tests/data/boost' no previously-included directories found matching 'scipy/special/tests/data/gsl' no previously-included directories found matching 'scipy/special/tests/data/local' no previously-included directories found matching 'doc/build' no previously-included directories found matching 'doc/source/generated' no previously-included directories found matching '*/__pycache__' warning: no previously-included files matching '*~' found anywhere in distribution warning: no previously-included files matching '*.bak' found anywhere in distribution warning: no previously-included files matching '*.swp' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution writing manifest file 'pip-egg-info/scipy.egg-info/SOURCES.txt' Source in /tmp/pip-req-build-wvhwk4 has version 1.1.0, which satisfies requirement scipy==1.1.0 from file:///usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0/src Removed scipy==1.1.0 from file:///usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0/src from build tracker '/tmp/pip-req-tracker-SwH_RJ' Installing collected packages: scipy Created temporary directory: /tmp/pip-record-51znTB Running setup.py install for scipy: started Running command /usr/local/src/Misc/sage-8.6/local/bin/python2 -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-wvhwk4/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" --no-user-cfg install --record /tmp/pip-record-51znTB/install-record.txt --single-version-externally-managed --root /usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0/inst --compile Note: if you need reliable uninstall behavior, then install with pip instead of using `setup.py install`: - `pip install .` (from a git repo or downloaded source release) - `pip install scipy` (last SciPy release on PyPI) Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-req-build-wvhwk4/setup.py", line 474, in <module> setup_package() File "/tmp/pip-req-build-wvhwk4/setup.py", line 450, in setup_package from numpy.distutils.core import setup File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/numpy/__init__.py", line 142, in <module> from . import add_newdocs File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module> from numpy.lib import add_newdoc File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8, in <module> from .type_check import * File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in <module> import numpy.core.numeric as _nx File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/numpy/core/__init__.py", line 26, in <module> raise ImportError(msg) ImportError: Importing the multiarray numpy extension module failed. Most likely you are trying to import a failed build of numpy. If you're working with a numpy git repo, try `git clean -xdf` (removes all files not under version control). Otherwise reinstall numpy. Original error was: libgfortran.so.3: cannot open shared object file: No such file or directory Running setup.py install for scipy: finished with status 'error' Cleaning up... Removing source in /tmp/pip-req-build-wvhwk4 Removed build tracker '/tmp/pip-req-tracker-SwH_RJ' Command "/usr/local/src/Misc/sage-8.6/local/bin/python2 -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-wvhwk4/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" --no-user-cfg install --record /tmp/pip-record-51znTB/install-record.txt --single-version-externally-managed --root /usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0/inst --compile" failed with error code 1 in /tmp/pip-req-build-wvhwk4/ Exception information: Traceback (most recent call last): File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/pip/_internal/basecommand.py", line 141, in main status = self.run(options, args) File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/pip/_internal/commands/install.py", line 347, in run use_user_site=options.use_user_site, File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/pip/_internal/req/__init__.py", line 49, in install_given_reqs **kwargs File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/pip/_internal/req/req_install.py", line 972, in install spinner=spinner, File "/usr/local/src/Misc/sage-8.6/local/lib/python2.7/site-packages/pip/_internal/utils/misc.py", line 701, in call_subprocess % (command_desc, proc.returncode, cwd)) InstallationError: Command "/usr/local/src/Misc/sage-8.6/local/bin/python2 -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-wvhwk4/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" --no-user-cfg install --record /tmp/pip-record-51znTB/install-record.txt --single-version-externally-managed --root /usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0/inst --compile" failed with error code 1 in /tmp/pip-req-build-wvhwk4/ Error: installing with pip2 failed ******************************************************************************** Error installing scipy-1.1.0 ******************************************************************************** real 0m8.611s user 0m6.527s sys 0m1.531s ************************************************************************ Error installing package scipy-1.1.0 ************************************************************************ Please email sage-devel (http://groups.google.com/group/sage-devel) explaining the problem and including the log file /usr/local/src/Misc/sage-8.6/logs/pkgs/scipy-1.1.0.log Describe your computer, operating system, etc. If you want to try to fix the problem yourself, *don't* just cd to /usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0 and type 'make' or whatever is appropriate. Instead, the following commands setup all environment variables correctly and load a subshell for you to debug the error: (cd '/usr/local/src/Misc/sage-8.6/local/var/tmp/sage/build/scipy-1.1.0' && '/usr/local/src/Misc/sage-8.6/sage' --sh) When you are done debugging, you can type "exit" to leave the subshell. ************************************************************************
