I have upgraded pip after the error and it didn't change, I have no issues installing scipy locally, I have gcc 4.8, I have the latest version of gfortran (4.8.4), I tried this fancy gfortran installation which seems to be specific to Ubuntu and it did install something, I tried git pull heroku master but get fatal: Coundn't find remote ref master, adding the --rebase option returns the same error. This makes sense I think since I used the following to delete all apps on Heroku so there shouldn't be anything to pull: for app in $(heroku apps); do heroku apps:destroy --app $app --confirm $app; done
The links all link to solutions that purportedly work for what appears to my problem as well or highly similar
I'd like to note that my app has been deployed successfully before many months ago. Changes I made include: I modified the code a bit - compiles and runs locally, I want to now add a ~500MB .tiff as well to the site so used git add and committed it as if it were any other file. I read somewhere that users have 200MB what I believe is called slug space and GB upon GB of space in a tmp folder so I didn't think space would be an issue. I also reinitialized git as I needed to work from a different directory, but since I deleted all the apps from Heroku I figured no merges would need to be performed (trying to have a fresh start)
Command:
git push heroku master -f
Result with the first error message I saw close to the top:
remote: customize IntelFCompiler
remote: Could not locate executable ifort
remote: Could not locate executable ifc
remote: customize LaheyFCompiler
remote: Could not locate executable lf95
remote: customize PGroupFCompiler
remote: Could not locate executable pgfortran
remote: customize AbsoftFCompiler
remote: Could not locate executable f90
remote: Could not locate executable f77
remote: customize NAGFCompiler
remote: customize VastFCompiler
remote: customize CompaqFCompiler
remote: Could not locate executable fort
remote: customize IntelItaniumFCompiler
remote: Could not locate executable efort
remote: Could not locate executable efc
remote: customize IntelEM64TFCompiler
remote: customize GnuFCompiler
remote: Could not locate executable g77
remote: customize G95FCompiler
remote: Could not locate executable g95
remote: customize PathScaleFCompiler
remote: Could not locate executable pathf95
remote: don't know how to compile Fortran code on platform 'posix'
remote: building 'dfftpack' library
remote: error: library dfftpack has Fortran sources but no Fortran compiler found
remote:
remote: ----------------------------------------
remote: Running setup.py clean for scipy
remote: Running setup.py bdist_wheel for matplotlib: started
remote: Running setup.py bdist_wheel for matplotlib: finished with status 'done'
remote: Stored in directory: /app/.cache/pip/wheels/94/22/76/2f17479b2ff90623041a1ce6b6c2b88bcd68e4a24dd2456d9f
remote: Running setup.py bdist_wheel for parmap: started
remote: Running setup.py bdist_wheel for parmap: finished with status 'done'
remote: Stored in directory: /app/.cache/pip/wheels/74/fd/cf/7d03cee9ca1d249a13c3b68e2743dd2127b4c123f632a4a846
remote: Running setup.py bdist_wheel for DataSpyre: started
remote: Running setup.py bdist_wheel for DataSpyre: finished with status 'done'
remote: Stored in directory: /app/.cache/pip/wheels/b0/ad/2c/f854c06dd738eec9ba91b4798c871cf078cc699bf7b153988c
remote: Running setup.py bdist_wheel for pandas: started
remote: Running setup.py bdist_wheel for pandas: still running...
remote: Running setup.py bdist_wheel for pandas: still running...
remote: Running setup.py bdist_wheel for pandas: finished with status 'done'
remote: Stored in directory: /app/.cache/pip/wheels/21/92/81/0259bc54d3f52003b6b94825569abf890237f20c2122a2af4f
remote: Running setup.py bdist_wheel for cherrypy: started
remote: Running setup.py bdist_wheel for cherrypy: finished with status 'done'
remote: Stored in directory: /app/.cache/pip/wheels/b3/2e/4a/4d94757218472574adad901b155f3fcbd5290a86da272543c9
remote: Running setup.py bdist_wheel for MarkupSafe: started
remote: Running setup.py bdist_wheel for MarkupSafe: finished with status 'done'
remote: Stored in directory: /app/.cache/pip/wheels/94/a7/79/f79a998b64c1281cb99fa9bbd33cfc9b8b5775f438218d17a7
remote: Successfully built matplotlib parmap DataSpyre pandas cherrypy MarkupSafe
remote: Failed to build scipy
remote: Installing collected packages: scipy, six, python-dateutil, pytz, cycler, pyparsing, matplotlib, parmap, pandas, cherrypy, MarkupSafe, jinja2, DataSpyre
remote: Running setup.py install for scipy: started
remote: Running setup.py install for scipy: finished with status 'error'
remote: Complete output from command /app/.heroku/miniconda/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-IpiQEw/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-09yK_9-record/install-record.txt --single-version-externally-managed --compile:
remote: lapack_opt_info:
remote: openblas_lapack_info:
remote: libraries openblas not found in ['/app/.heroku/miniconda/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
remote: NOT AVAILABLE
remote:
remote: lapack_mkl_info:
remote: mkl_info:
remote: /app/.heroku/miniconda/lib/python2.7/site-packages/numpy/distutils/system_info.py:635: UserWarning: Specified path is invalid.
remote: warnings.warn('Specified path %s is invalid.' % d)
remote: FOUND:
remote: libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'iomp5', 'pthread']
remote: library_dirs = ['/app/.heroku/miniconda/lib']
remote: define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
remote: include_dirs = ['/app/.heroku/miniconda/include']
remote:
remote: FOUND:
remote: libraries = ['mkl_lapack95_lp64', 'mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'iomp5', 'pthread']
remote: library_dirs = ['/app/.heroku/miniconda/lib']
remote: define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
remote: include_dirs = ['/app/.heroku/miniconda/include']
remote:
remote: FOUND:
remote: libraries = ['mkl_lapack95_lp64', 'mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'iomp5', 'pthread']
remote: library_dirs = ['/app/.heroku/miniconda/lib']
remote: define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
remote: include_dirs = ['/app/.heroku/miniconda/include']
remote:
remote: Running from scipy source directory.
remote: Splitting linalg.interpolative Fortran source files
remote: /app/.heroku/miniconda/lib/python2.7/site-packages/numpy/distutils/system_info.py:635: UserWarning: Specified path /usr/local/include/python2.7 is invalid.
remote: warnings.warn('Specified path %s is invalid.' % d)
remote: blas_opt_info:
remote: blas_mkl_info:
remote: FOUND:
remote: libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'iomp5', 'pthread']
remote: library_dirs = ['/app/.heroku/miniconda/lib']
remote: define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
remote: include_dirs = ['/app/.heroku/miniconda/include']
remote:
remote: FOUND:
remote: libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'iomp5', 'pthread']
remote: library_dirs = ['/app/.heroku/miniconda/lib']
remote: define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
remote: include_dirs = ['/app/.heroku/miniconda/include']
remote:
remote: running install
remote: running build
remote: running config_cc
remote: unifing config_cc, config, build_clib, build_ext, build commands --compiler options
remote: running config_fc
remote: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
remote: running build_src
remote: build_src
remote: building py_modules sources
remote: building library "dfftpack" sources
remote: building library "fftpack" sources
remote: building library "mach" sources
remote: building library "quadpack" sources
remote: building library "odepack" sources
remote: building library "dop" sources
remote: building library "fitpack" sources
remote: building library "fwrappers" sources
remote: building library "odrpack" sources
remote: building library "minpack" sources
remote: building library "rootfind" sources
remote: building library "superlu_src" sources
remote: building library "arpack_scipy" sources
remote: building library "sc_c_misc" sources
remote: building library "sc_cephes" sources
remote: building library "sc_mach" sources
remote: building library "sc_amos" sources
remote: building library "sc_cdf" sources
remote: building library "sc_specfun" sources
remote: building library "statlib" sources
remote: building extension "scipy.cluster._vq" sources
remote: building extension "scipy.cluster._hierarchy" sources
remote: building extension "scipy.fftpack._fftpack" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: building extension "scipy.fftpack.convolve" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: building extension "scipy.integrate._quadpack" sources
remote: building extension "scipy.integrate._odepack" sources
remote: building extension "scipy.integrate.vode" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: building extension "scipy.integrate.lsoda" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: building extension "scipy.integrate._dop" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: building extension "scipy.integrate._test_multivariate" sources
remote: building extension "scipy.integrate._test_odeint_banded" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: adding 'build/src.linux-x86_64-2.7/scipy/integrate/_test_odeint_banded-f2pywrappers.f' to sources.
remote: building extension "scipy.interpolate.interpnd" sources
remote: building extension "scipy.interpolate._ppoly" sources
remote: building extension "scipy.interpolate._fitpack" sources
remote: building extension "scipy.interpolate.dfitpack" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: adding 'build/src.linux-x86_64-2.7/scipy/interpolate/src/dfitpack-f2pywrappers.f' to sources.
remote: building extension "scipy.interpolate._interpolate" sources
remote: building extension "scipy.io.matlab.streams" sources
remote: building extension "scipy.io.matlab.mio_utils" sources
remote: building extension "scipy.io.matlab.mio5_utils" sources
remote: building extension "scipy.linalg._fblas" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/linalg/_fblas-f2pywrappers.f' to sources.
remote: building extension "scipy.linalg._flapack" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/linalg/_flapack-f2pywrappers.f' to sources.
remote: building extension "scipy.linalg._flinalg" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: building extension "scipy.linalg._interpolative" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: building extension "scipy.linalg._calc_lwork" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: building extension "scipy.linalg._solve_toeplitz" sources
remote: building extension "scipy.linalg.cython_blas" sources
remote: building extension "scipy.linalg.cython_lapack" sources
remote: building extension "scipy.linalg._decomp_update" sources
remote: building extension "scipy.odr.__odrpack" sources
remote: building extension "scipy.optimize._minpack" sources
remote: building extension "scipy.optimize._zeros" sources
remote: building extension "scipy.optimize._lbfgsb" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: building extension "scipy.optimize.moduleTNC" sources
remote: building extension "scipy.optimize._cobyla" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: building extension "scipy.optimize.minpack2" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: building extension "scipy.optimize._slsqp" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: building extension "scipy.optimize._nnls" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: building extension "scipy.optimize._group_columns" sources
remote: building extension "scipy.optimize._lsq.givens_elimination" sources
remote: building extension "scipy.signal.sigtools" sources
remote: building extension "scipy.signal._spectral" sources
remote: building extension "scipy.signal._max_len_seq_inner" sources
remote: building extension "scipy.signal.spline" sources
remote: building extension "scipy.sparse.linalg.isolve._iterative" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: building extension "scipy.sparse.linalg.dsolve._superlu" sources
remote: building extension "scipy.sparse.linalg.eigen.arpack._arpack" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/sparse/linalg/eigen/arpack/_arpack-f2pywrappers.f' to sources.
remote: building extension "scipy.sparse.csgraph._shortest_path" sources
remote: building extension "scipy.sparse.csgraph._traversal" sources
remote: building extension "scipy.sparse.csgraph._min_spanning_tree" sources
remote: building extension "scipy.sparse.csgraph._reordering" sources
remote: building extension "scipy.sparse.csgraph._tools" sources
remote: building extension "scipy.sparse._csparsetools" sources
remote: building extension "scipy.sparse._sparsetools" sources
remote: [generate_sparsetools] 'scipy/sparse/sparsetools/bsr_impl.h' already up-to-date
remote: [generate_sparsetools] 'scipy/sparse/sparsetools/csr_impl.h' already up-to-date
remote: [generate_sparsetools] 'scipy/sparse/sparsetools/csc_impl.h' already up-to-date
remote: [generate_sparsetools] 'scipy/sparse/sparsetools/other_impl.h' already up-to-date
remote: [generate_sparsetools] 'scipy/sparse/sparsetools/sparsetools_impl.h' already up-to-date
remote: building extension "scipy.spatial.qhull" sources
remote: building extension "scipy.spatial.ckdtree" sources
remote: building extension "scipy.spatial._distance_wrap" sources
remote: building extension "scipy.special.specfun" sources
remote: f2py options: ['--no-wrap-functions']
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: building extension "scipy.special._ufuncs" sources
remote: building extension "scipy.special._ufuncs_cxx" sources
remote: building extension "scipy.special._ellip_harm_2" sources
remote: building extension "scipy.stats.statlib" sources
remote: f2py options: ['--no-wrap-functions']
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: building extension "scipy.stats.vonmises_cython" sources
remote: building extension "scipy.stats._rank" sources
remote: building extension "scipy.stats.mvn" sources
remote: f2py options: []
remote: adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
remote: adding 'build/src.linux-x86_64-2.7' to include_dirs.
remote: adding 'build/src.linux-x86_64-2.7/scipy/stats/mvn-f2pywrappers.f' to sources.
remote: building extension "scipy.ndimage._nd_image" sources
remote: building extension "scipy.ndimage._ni_label" sources
remote: building data_files sources
remote: build_src: building npy-pkg config files
remote: running build_py
remote: copying scipy/version.py -> build/lib.linux-x86_64-2.7/scipy
remote: copying build/src.linux-x86_64-2.7/scipy/__config__.py -> build/lib.linux-x86_64-2.7/scipy
remote: running build_clib
remote: customize UnixCCompiler
remote: customize UnixCCompiler using build_clib
remote: customize Gnu95FCompiler
remote: Could not locate executable gfortran
remote: Could not locate executable f95
remote: customize IntelFCompiler
remote: Could not locate executable ifort
remote: Could not locate executable ifc
remote: customize LaheyFCompiler
remote: Could not locate executable lf95
remote: customize PGroupFCompiler
remote: Could not locate executable pgfortran
remote: customize AbsoftFCompiler
remote: Could not locate executable f90
remote: Could not locate executable f77
remote: customize NAGFCompiler
remote: customize VastFCompiler
remote: customize CompaqFCompiler
remote: Could not locate executable fort
remote: customize IntelItaniumFCompiler
remote: Could not locate executable efort
remote: Could not locate executable efc
remote: customize IntelEM64TFCompiler
remote: customize GnuFCompiler
remote: Could not locate executable g77
remote: customize G95FCompiler
remote: Could not locate executable g95
remote: customize PathScaleFCompiler
remote: Could not locate executable pathf95
remote: don't know how to compile Fortran code on platform 'posix'
remote: building 'dfftpack' library
remote: error: library dfftpack has Fortran sources but no Fortran compiler found
remote:
remote: ----------------------------------------
remote: Command "/app/.heroku/miniconda/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-IpiQEw/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-09yK_9-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-IpiQEw/scipy
remote:
remote: ! Push rejected, failed to compile Python/Conda app
remote:
remote: Verifying deploy...
remote:
remote: ! Push rejected to brain-image-analyzer.
remote:
To https://git.heroku.com/brain-image-analyzer.git
! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'https://git.heroku.com/brain-image-analyzer.git'
I am sadly not using a well-known framework like Django or Flask and instead using Spyre and am following deployment instructions from here which have worked for me before
Do I need to make a symbolic link...? Maybe it is looking in the wrong place and I need to force it to the Fortran compiler by unceremoniously teleporting it there? This is the only thing I can think of I haven't tried. I just don't know where to point the link though.
