Sage installation error during relocate

after running the relocate script as root

$ sudo chown -R USER:USER .sage (replace USER by actual user name)

error message

Rewriting paths for your new installation directory
===================================================

This might take a few minutes but only has to be done once.

patching /usr/lib/sagemath/src/build/cythonized/sage/rings/real_arb.c
Traceback (most recent call last):
  File "/usr/lib/sagemath/relocate-once.py", line 85, in <module>
    p('src/build/cythonized/sage/rings/real_arb.c').substitute().save()
  File "/usr/lib/sagemath/relocate-once.py", line 70, in __call__
    return FilePatch(self, filename)
  File "/usr/lib/sagemath/relocate-once.py", line 21, in __init__
    self.st = os.stat(filename)
OSError: [Errno 2] No such file or directory: '/usr/lib/sagemath/src/build/cythonized/sage/rings/real_arb.c'
┌────────────────────────────────────────────────────────────────────┐
│ SageMath Version 7.0, Release Date: 2016-01-19                     │
│ Type "notebook()" for the browser-based notebook interface.        │
│ Type "help()" for help.                                            │
└────────────────────────────────────────────────────────────────────┘

last part of replacing operation output

patching /usr/lib/sagemath/local/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/liblto_plugin.la
not found /usr/lib/sagemath/local/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/liblto_plugin.la
patching /usr/lib/sagemath/local/libexec/git-core/git-credential-cache--daemon
not found /usr/lib/sagemath/local/libexec/git-core/git-credential-cache--daemon
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/graphs/base/dense_graph.so
patching /usr/lib/sagemath/local/bin/allfaces_gmp
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/libs/singular/groebner_strategy.so
patching /usr/lib/sagemath/local/lib/libatomic.so.1.1.0
patching /usr/lib/sagemath/src/build/cythonized/sage/coding/codecan/codecan.c
not found /usr/lib/sagemath/src/build/cythonized/sage/coding/codecan/codecan.c
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/combinat/matrices/dancing_links.so
patching /usr/lib/sagemath/local/lib/libppl_c.so.4.0.0
patching /usr/lib/sagemath/local/include/atlas/atlas_ssyr2_L1.h
patching /usr/lib/sagemath/local/bin/x86_64-unknown-linux-gnu-gfortran
patching /usr/lib/sagemath/local/gap/gap-4.7.9/bin/x86_64-unknown-linux-gnu-gcc-default64/c_random.o
patching /usr/lib/sagemath/local/share/terminfo/t/tvi912c-unk
patching /usr/lib/sagemath/src/build/cythonized/sage/ext/interpreters/wrapper_el.c
not found /usr/lib/sagemath/src/build/cythonized/sage/ext/interpreters/wrapper_el.c
patching /usr/lib/sagemath/src/build/cythonized/sage/misc/function_mangling.c
not found /usr/lib/sagemath/src/build/cythonized/sage/misc/function_mangling.c
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/libs/ecl.so
patching /usr/lib/sagemath/local/lib/pkgconfig/libpng12.pc
patching /usr/lib/sagemath/local/lib/libform.so.5.9
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.matrix.matrix_rational_sparse
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.matrix.matrix_rational_sparse
patching /usr/lib/sagemath/local/lib/python2.7/lib-dynload/_json.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/combinat/dict_addition.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/groups/group.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/graphs/trees.so
patching /usr/lib/sagemath/local/share/terminfo/v/vt200-old
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.ext.interrupt.interrupt
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.ext.interrupt.interrupt
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/rings/finite_rings/integer_mod.so
patching /usr/lib/sagemath/local/lib/omalloc_debug.o
patching /usr/lib/sagemath/local/lib/python2.7/config/Makefile
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/ext/memory.so
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.graphs.graph_decompositions.cutwidth
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.graphs.graph_decompositions.cutwidth
patching /usr/lib/sagemath/src/build/cythonized/sage/misc/reset.c
not found /usr/lib/sagemath/src/build/cythonized/sage/misc/reset.c
patching /usr/lib/sagemath/src/build/cythonized/sage/misc/cachefunc.c
not found /usr/lib/sagemath/src/build/cythonized/sage/misc/cachefunc.c
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.padics.pow_computer
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.padics.pow_computer
patching /usr/lib/sagemath/local/lib/ecl-15.3.7/rt.fas
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.symbolic.ring
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.symbolic.ring
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/matrix/matrix_rational_dense.so
patching /usr/lib/sagemath/src/build/cythonized/sage/combinat/designs/evenly_distributed_sets.c
not found /usr/lib/sagemath/src/build/cythonized/sage/combinat/designs/evenly_distributed_sets.c
patching /usr/lib/sagemath/src/build/cythonized/sage/rings/real_double.c
not found /usr/lib/sagemath/src/build/cythonized/sage/rings/real_double.c
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.algebras.letterplace.letterplace_ideal
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.algebras.letterplace.letterplace_ideal
patching /usr/lib/sagemath/src/build/cythonized/sage/gsl/dwt.c
not found /usr/lib/sagemath/src/build/cythonized/sage/gsl/dwt.c
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.combinat.debruijn_sequence
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.combinat.debruijn_sequence
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.matrix.matrix_window
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.matrix.matrix_window
patching /usr/lib/sagemath/local/libexec/git-core/git-cvsexportcommit
not found /usr/lib/sagemath/local/libexec/git-core/git-cvsexportcommit
patching /usr/lib/sagemath/local/lib/python2.7/config/python.o
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/combinat/debruijn_sequence.so
patching /usr/lib/sagemath/local/lib/pkgconfig/zlib.pc
patching /usr/lib/sagemath/src/build/cythonized/sage/gsl/callback.c
not found /usr/lib/sagemath/src/build/cythonized/sage/gsl/callback.c
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/graphs/graph_decompositions/graph_products.so
patching /usr/lib/sagemath/local/lib/libgmp.so.16.6.2
patching /usr/lib/sagemath/local/share/terminfo/n/news31-a
patching /usr/lib/sagemath/src/build/cythonized/sage/structure/coerce_dict.c
not found /usr/lib/sagemath/src/build/cythonized/sage/structure/coerce_dict.c
patching /usr/lib/sagemath/src/build/cythonized/sage/libs/ntl/ntl_GF2EContext.cpp
not found /usr/lib/sagemath/src/build/cythonized/sage/libs/ntl/ntl_GF2EContext.cpp
patching /usr/lib/sagemath/local/bin/bzip2recover
patching /usr/lib/sagemath/local/lib/libiml.so.0.1.1
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.graphs.base.static_sparse_graph
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.graphs.base.static_sparse_graph
patching /usr/lib/sagemath/local/lib/ecl-15.3.7/ecl-cdb.fas
patching /usr/lib/sagemath/local/lib/R/bin/exec/R
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.matrix.matrix_cyclo_dense
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.matrix.matrix_cyclo_dense
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/symbolic/substitution_map.so
patching /usr/lib/sagemath/local/bin/testshoot
patching /usr/lib/sagemath/src/build/cythonized/sage/combinat/debruijn_sequence.c
not found /usr/lib/sagemath/src/build/cythonized/sage/combinat/debruijn_sequence.c
patching /usr/lib/sagemath/src/build/cythonized/sage/parallel/safefork.c
not found /usr/lib/sagemath/src/build/cythonized/sage/parallel/safefork.c
patching /usr/lib/sagemath/local/share/terminfo/h/hp2392
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.libs.coxeter3.coxeter
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.libs.coxeter3.coxeter
patching /usr/lib/sagemath/src/build/cythonized/sage/modular/modform/eis_series_cython.c
not found /usr/lib/sagemath/src/build/cythonized/sage/modular/modform/eis_series_cython.c
patching /usr/lib/sagemath/src/build/cythonized/sage/groups/perm_gps/partn_ref/canonical_augmentation.c
not found /usr/lib/sagemath/src/build/cythonized/sage/groups/perm_gps/partn_ref/canonical_augmentation.c
patching /usr/lib/sagemath/local/share/terminfo/n/nwp514-o
patching /usr/lib/sagemath/src/build/cythonized/sage/misc/weak_dict.c
not found /usr/lib/sagemath/src/build/cythonized/sage/misc/weak_dict.c
patching /usr/lib/sagemath/local/share/terminfo/v/vt400-24
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/Cython-0.23.3-py2.7-linux-x86_64.egg/Cython/Plex/Actions.so
patching /usr/lib/sagemath/src/build/cythonized/sage/libs/ecl.c
not found /usr/lib/sagemath/src/build/cythonized/sage/libs/ecl.c
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/graphs/graph_decompositions/rankwidth.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/rings/padics/local_generic_element.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/rings/polynomial/polynomial_compiled.so
patching /usr/lib/sagemath/local/share/terminfo/t/tvi912b-mc
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/libs/ntl/ntl_GF2EContext.so
patching /usr/lib/sagemath/src/build/cythonized/sage/matroids/basis_matroid.c
not found /usr/lib/sagemath/src/build/cythonized/sage/matroids/basis_matroid.c
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/rings/power_series_poly.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/scipy/linalg/_flinalg.so
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.structure.coerce_actions
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.structure.coerce_actions
patching /usr/lib/sagemath/local/lib/python2.7/lib-dynload/_hashlib.so
patching /usr/lib/sagemath/src/build/cythonized/sage/stats/hmm/util.c
not found /usr/lib/sagemath/src/build/cythonized/sage/stats/hmm/util.c
patching /usr/lib/sagemath/src/build/cythonized/sage/matrix/matrix_double_dense.c
not found /usr/lib/sagemath/src/build/cythonized/sage/matrix/matrix_double_dense.c
patching /usr/lib/sagemath/src/build/cythonized/sage/rings/polynomial/symmetric_reduction.c
not found /usr/lib/sagemath/src/build/cythonized/sage/rings/polynomial/symmetric_reduction.c
patching /usr/lib/sagemath/local/lib/python2.7/lib-dynload/bz2.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/rings/padics/padic_ZZ_pX_element.so
patching /usr/lib/sagemath/src/build/cythonized/sage/rings/finite_rings/integer_mod.c
not found /usr/lib/sagemath/src/build/cythonized/sage/rings/finite_rings/integer_mod.c
patching /usr/lib/sagemath/src/build/cythonized/sage/libs/eclib/homspace.cpp
not found /usr/lib/sagemath/src/build/cythonized/sage/libs/eclib/homspace.cpp
patching /usr/lib/sagemath/local/include/atlas/atlas_zsyr.h
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.factorint
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.factorint
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/Cython-0.23.3-py2.7-linux-x86_64.egg/Cython/Compiler/Lexicon.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/algebras/letterplace/free_algebra_element_letterplace.so
patching /usr/lib/sagemath/local/lib/R/etc/ldpaths
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.quadratic_forms.count_local_2
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.quadratic_forms.count_local_2
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.libs.eclib.mat
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.libs.eclib.mat
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.ext.memory_allocator
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.ext.memory_allocator
patching /usr/lib/sagemath/local/lib/ecl-15.3.7/libserve-event.a
patching /usr/lib/sagemath/local/share/terminfo/a/altos5
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/scipy/io/matlab/streams.so
patching /usr/lib/sagemath/local/include/atlas/atlas_dsyr.h
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.plot.plot3d.parametric_surface
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.plot.plot3d.parametric_surface
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.combinat.words.word_datatypes
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.combinat.words.word_datatypes
patching /usr/lib/sagemath/src/build/cythonized/sage/modular/arithgroup/arithgroup_element.c
not found /usr/lib/sagemath/src/build/cythonized/sage/modular/arithgroup/arithgroup_element.c
patching /usr/lib/sagemath/local/share/terminfo/n/news-42-sjis
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.gsl.dwt
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.gsl.dwt
patching /usr/lib/sagemath/local/bin/fplll
patching /usr/lib/sagemath/local/lib/pkgconfig/libR.pc
patching /usr/lib/sagemath/local/lib/python2.7/lib-dynload/unicodedata.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/misc/derivative.so
patching /usr/lib/sagemath/local/lib/pkgconfig/pynac.pc
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/PIL/_imagingtk.so
patching /usr/lib/sagemath/src/build/cythonized/sage/sat/solvers/cryptominisat/cryptominisat.cpp
not found /usr/lib/sagemath/src/build/cythonized/sage/sat/solvers/cryptominisat/cryptominisat.cpp
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.groups.perm_gps.partn_ref2.refinement_generic
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.groups.perm_gps.partn_ref2.refinement_generic
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.graphs.base.dense_graph
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.graphs.base.dense_graph
patching /usr/lib/sagemath/local/lib/R/library/utils/libs/utils.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/modular/arithgroup/farey_symbol.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/Crypto/Cipher/_AES.so
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.combinat.enumeration_mod_permgroup
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.combinat.enumeration_mod_permgroup
patching /usr/lib/sagemath/local/lib/libgap.so.0.0.0
patching /usr/lib/sagemath/local/lib/python2.7/lib-dynload/time.so
patching /usr/lib/sagemath/src/build/cythonized/sage/numerical/backends/glpk_backend.cpp
not found /usr/lib/sagemath/src/build/cythonized/sage/numerical/backends/glpk_backend.cpp
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.stats.hmm.distributions
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.stats.hmm.distributions
patching /usr/lib/sagemath/local/share/terminfo/v/vt320-k311
patching /usr/lib/sagemath/local/share/terminfo/h/he80
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/Crypto/Util/strxor.so
patching /usr/lib/sagemath/local/bin/libparse
patching /usr/lib/sagemath/local/bin/x86_64-unknown-linux-gnu-gcc-nm
patching /usr/lib/sagemath/src/build/cythonized/sage/gsl/fft.c
not found /usr/lib/sagemath/src/build/cythonized/sage/gsl/fft.c
patching /usr/lib/sagemath/src/build/cythonized/sage/rings/fraction_field_element.c
not found /usr/lib/sagemath/src/build/cythonized/sage/rings/fraction_field_element.c
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/scipy/optimize/_cobyla.so
patching /usr/lib/sagemath/local/share/terminfo/t/tvi920b-2p-p
patching /usr/lib/sagemath/local/lib/python2.7/lib-dynload/fcntl.so
patching /usr/lib/sagemath/local/lib/ecl-15.3.7/ecl-help.fas
patching /usr/lib/sagemath/local/lib/R/lib/libR.so
patching /usr/lib/sagemath/local/lib/libreadline.so.6.3
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/numpy/core/test_rational.so
patching /usr/lib/sagemath/local/bin/projection_gmp
patching /usr/lib/sagemath/src/build/cythonized/sage/libs/mpmath/utils.c
not found /usr/lib/sagemath/src/build/cythonized/sage/libs/mpmath/utils.c
patching /usr/lib/sagemath/src/build/cythonized/sage/libs/ntl/ntl_GF2X.cpp
not found /usr/lib/sagemath/src/build/cythonized/sage/libs/ntl/ntl_GF2X.cpp
patching /usr/lib/sagemath/local/gap/gap-4.7.9/bin/x86_64-unknown-linux-gnu-gcc-default64/cyclotom.o
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/ext/interactive_constructors_c.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/rings/polynomial/multi_polynomial_ideal_libsingular.so
patching /usr/lib/sagemath/local/share/terminfo/p/pcvt25-color
patching /usr/lib/sagemath/local/bin/gcc-ranlib
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.modules.vector_mod2_dense
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.modules.vector_mod2_dense
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.sat.solvers.cryptominisat.solverconf
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.sat.solvers.cryptominisat.solverconf
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.numerical.backends.ppl_backend
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.numerical.backends.ppl_backend
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.structure.misc
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.structure.misc
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.matrix.matrix_integer_dense
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.matrix.matrix_integer_dense
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.libs.ntl.ntl_ZZ_pEX
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.libs.ntl.ntl_ZZ_pEX
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.groups.perm_gps.partn_ref.refinement_python
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.groups.perm_gps.partn_ref.refinement_python
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/numpy/distutils/__config__.py
patching /usr/lib/sagemath/local/bin/gfortran
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.libs.pari.gen
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.libs.pari.gen
patching /usr/lib/sagemath/src/build/cythonized/sage/stats/hmm/chmm.c
not found /usr/lib/sagemath/src/build/cythonized/sage/stats/hmm/chmm.c
patching /usr/lib/sagemath/local/lib/R/library/grDevices/libs/grDevices.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/graphs/base/static_sparse_graph.so
patching /usr/lib/sagemath/src/build/cythonized/sage/misc/c3_controlled.c
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patching /usr/lib/sagemath/local/share/terminfo/n/ncsa-m-ns
patching /usr/lib/sagemath/local/share/terminfo/t/tvi912c-mc-vb
patching /usr/lib/sagemath/src/build/cythonized/sage/libs/singular/option.cpp
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patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/matroids/circuit_closures_matroid.so
patching /usr/lib/sagemath/local/share/terminfo/n/news31
patching /usr/lib/sagemath/local/bin/gcc
patching /usr/lib/sagemath/local/include/atlas/atlas_cmvtkernels.h
patching /usr/lib/sagemath/local/share/terminfo/g/go140w
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.graphs.genus
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patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/libs/symmetrica/symmetrica.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/ext/fast_eval.so
patching /usr/lib/sagemath/local/include/atlas/atlas_zher2_L1.h
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/graphs/cliquer.so
patching /usr/lib/sagemath/local/bin/git
patching /usr/lib/sagemath/local/bin/mcube
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.padics.morphism
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patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/libs/fplll/fplll.so
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.polynomial.multi_polynomial
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patching /usr/lib/sagemath/local/lib/libssp.so.0.0.0
patching /usr/lib/sagemath/local/libexec/git-core/git-svn
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patching /usr/lib/sagemath/local/share/terminfo/t/tvi920b-p-2p
patching /usr/lib/sagemath/local/lib/python2.7/lib-dynload/_sha.so
patching /usr/lib/sagemath/local/share/terminfo/i/ims-ansi
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patching /usr/lib/sagemath/src/build/cythonized/sage/misc/lazy_attribute.c
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patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.libs.libecm
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patching /usr/lib/sagemath/local/gap/gap-4.7.9/bin/x86_64-unknown-linux-gnu-gcc-default64/trans.o
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.schemes.projective.projective_morphism_helper
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patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.gsl.gsl_array
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patching /usr/lib/sagemath/local/share/terminfo/t/tvi920b-2p-mc
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patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/graphs/strongly_regular_db.so
patching /usr/lib/sagemath/local/lib/R/library/tcltk/libs/tcltk.so
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patching /usr/lib/sagemath/local/share/terminfo/h/hp2645a
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patching /usr/lib/sagemath/local/include/atlas/atlas_ssyr_L2.h
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patching /usr/lib/sagemath/local/lib/libm4ri-0.0.20140914.so
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patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/combinat/designs/evenly_distributed_sets.so
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patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/libs/singular/function.so
patching /usr/lib/sagemath/local/lib/libhistory.so.6.3
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/repl/inputhook.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/stats/intlist.so
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.algebras.letterplace.free_algebra_element_letterplace
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patching /usr/lib/sagemath/local/lib/python2.7/lib-dynload/math.so
patching /usr/lib/sagemath/src/build/cythonized/sage/graphs/graph_decompositions/graph_products.c
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patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/rings/number_field/totallyreal.so
patching /usr/lib/sagemath/local/share/terminfo/n/news-33-euc
patching /usr/lib/sagemath/local/lib/p_Procs_FieldIndep.so
patching /usr/lib/sagemath/src/build/cythonized/sage/rings/polynomial/cyclotomic.c
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patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.libs.readline
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patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.graphs.trees
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patching /usr/lib/sagemath/src/build/cythonized/sage/rings/function_field/function_field_element.c
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patching /usr/lib/sagemath/local/share/terminfo/n/nwp-517
patching /usr/lib/sagemath/local/lib/libplanarity.so.0.0.0
patching /usr/lib/sagemath/local/gap/gap-4.7.9/bin/x86_64-unknown-linux-gnu-gcc-default64/config.log
patching /usr/lib/sagemath/local/bin/adjacency
patching /usr/lib/sagemath/local/share/terminfo/n/nwp518-a
patching /usr/lib/sagemath/src/build/cythonized/sage/graphs/comparability.c
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patching /usr/lib/sagemath/local/gap/gap-4.7.9/bin/x86_64-unknown-linux-gnu-gcc-default64/read.o
patching /usr/lib/sagemath/local/lib/liblsan.so.0.0.0
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patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/sets/finite_set_map_cy.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/zmq/utils/compiler.json
patching /usr/lib/sagemath/src/build/cythonized/sage/libs/mpmath/ext_libmp.c
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patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/matrix/matrix1.so
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.structure.parent
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patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/rings/ring.so
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patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/categories/category_cy_helper.so
patching /usr/lib/sagemath/local/lib/python2.7/lib-dynload/readline.so
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patching /usr/lib/sagemath/local/lib/R/library/nlme/libs/nlme.so
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patching /usr/lib/sagemath/local/lib/python2.7/site-packages/Crypto/PublicKey/_fastmath.so
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patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/sets/recursively_enumerated_set.so
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patching /usr/lib/sagemath/local/include/atlas/atlas_cmvnkernels.h
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patching /usr/lib/sagemath/local/include/atlas/atlas_cher2_L1.h
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patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/numerical/linear_tensor_element.so
patching /usr/lib/sagemath/local/lib/liblapack.so.3.0.0
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/libs/mpmath/ext_main.so
patching /usr/lib/sagemath/local/libexec/git-core/git-cvsserver
not found /usr/lib/sagemath/local/libexec/git-core/git-cvsserver
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.categories.category_cy_helper
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.categories.category_cy_helper
patching /usr/lib/sagemath/src/build/cythonized/sage/groups/group.c
not found /usr/lib/sagemath/src/build/cythonized/sage/groups/group.c
patching /usr/lib/sagemath/local/share/terminfo/v/vt340
patching /usr/lib/sagemath/src/build/cythonized/sage/rings/polynomial/multi_polynomial_ideal_libsingular.cpp
not found /usr/lib/sagemath/src/build/cythonized/sage/rings/polynomial/multi_polynomial_ideal_libsingular.cpp
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/stats/hmm/util.so
patching /usr/lib/sagemath/local/share/terminfo/a/a210
patching /usr/lib/sagemath/local/lib/R/library/class/libs/class.so
patching /usr/lib/sagemath/local/share/terminfo/p/pcvt35
patching /usr/lib/sagemath/local/share/terminfo/n/nwp517-w
patching /usr/lib/sagemath/local/share/terminfo/p/pcvt40
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.real_interval_absolute
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.real_interval_absolute
patching /usr/lib/sagemath/src/build/cythonized/sage/graphs/base/static_sparse_backend.c
not found /usr/lib/sagemath/src/build/cythonized/sage/graphs/base/static_sparse_backend.c
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.modules.vector_rational_dense
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.modules.vector_rational_dense
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/modules/vector_double_dense.so
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.polynomial.polydict
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.polynomial.polydict
patching /usr/lib/sagemath/local/lib/ecl-15.3.7/ql-minitar.fas
patching /usr/lib/sagemath/local/bin/schubmult
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/gsl/probability_distribution.so
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.misc.session
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.misc.session
patching /usr/lib/sagemath/local/bin/TSingular
patching /usr/lib/sagemath/src/build/cythonized/sage/interfaces/sagespawn.c
not found /usr/lib/sagemath/src/build/cythonized/sage/interfaces/sagespawn.c
patching /usr/lib/sagemath/local/include/atlas/atlas_zr2kernels.h
patching /usr/lib/sagemath/src/build/cythonized/sage/libs/ntl/ntl_GF2EX.cpp
not found /usr/lib/sagemath/src/build/cythonized/sage/libs/ntl/ntl_GF2EX.cpp
patching /usr/lib/sagemath/local/share/terminfo/a/alt5
patching /usr/lib/sagemath/local/share/terminfo/v/vt330
patching /usr/lib/sagemath/src/build/cythonized/sage/ext/interrupt/interrupt.c
not found /usr/lib/sagemath/src/build/cythonized/sage/ext/interrupt/interrupt.c
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.polynomial.polynomial_real_mpfr_dense
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.polynomial.polynomial_real_mpfr_dense
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/libs/ntl/ntl_mat_GF2.so
patching /usr/lib/sagemath/local/share/terminfo/t/tvi920c-mc-2p
patching /usr/lib/sagemath/local/lib/python2.7/lib-dynload/_testcapi.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/zmq/backend/cython/utils.so
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.structure.parent_gens
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.structure.parent_gens
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/rings/semirings/tropical_semiring.so
patching /usr/lib/sagemath/src/build/cythonized/sage/graphs/distances_all_pairs.c
not found /usr/lib/sagemath/src/build/cythonized/sage/graphs/distances_all_pairs.c
patching /usr/lib/sagemath/local/gap/gap-4.7.9/Makefile-default64
patching /usr/lib/sagemath/local/lib/ecl-15.3.7/libdefsystem.a
patching /usr/lib/sagemath/local/bin/gdtopng
patching /usr/lib/sagemath/local/gap/gap-4.7.9/bin/x86_64-unknown-linux-gnu-gcc-default64/macfloat.o
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.ring
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.ring
patching /usr/lib/sagemath/src/build/cythonized/sage/numerical/backends/cvxopt_sdp_backend.c
not found /usr/lib/sagemath/src/build/cythonized/sage/numerical/backends/cvxopt_sdp_backend.c
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/media/channels.so
patching /usr/lib/sagemath/src/build/cythonized/sage/matrix/matrix_cyclo_dense.cpp
not found /usr/lib/sagemath/src/build/cythonized/sage/matrix/matrix_cyclo_dense.cpp
patching /usr/lib/sagemath/local/share/terminfo/t/tvi912c-mc-2p
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/matrix/matrix_cyclo_dense.so
patching /usr/lib/sagemath/local/bin/lcdd_gmp
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/graphs/base/boost_graph.so
patching /usr/lib/sagemath/local/gap/gap-4.7.9/bin/x86_64-unknown-linux-gnu-gcc-default64/opers.o
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/scipy/signal/sigtools.so
patching /usr/lib/sagemath/local/bin/ncursesw5-config
patching /usr/lib/sagemath/local/share/terminfo/t/tvi920c-unk
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/matrix/matrix_mod2_dense.so
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.polynomial.polynomial_rational_flint
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.polynomial.polynomial_rational_flint
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/quivers/algebra_elements.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/matrix/matrix_mpolynomial_dense.so
patching /usr/lib/sagemath/src/build/cythonized/sage/matrix/matrix_dense.c
not found /usr/lib/sagemath/src/build/cythonized/sage/matrix/matrix_dense.c
patching /usr/lib/sagemath/local/lib/ecl-15.3.7/asdf.fas
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.polynomial.multi_polynomial_ring_generic
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.polynomial.multi_polynomial_ring_generic
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.schemes.toric.divisor_class
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.schemes.toric.divisor_class
patching /usr/lib/sagemath/local/libexec/git-core/git-fast-import
not found /usr/lib/sagemath/local/libexec/git-core/git-fast-import
patching /usr/lib/sagemath/local/share/terminfo/t/tvi914
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/Crypto/Util/_counter.so
patching /usr/lib/sagemath/local/lib/libpanelw.so.5.9
patching /usr/lib/sagemath/local/share/terminfo/e/emu-220
patching /usr/lib/sagemath/src/build/cythonized/sage/misc/lazy_import.c
not found /usr/lib/sagemath/src/build/cythonized/sage/misc/lazy_import.c
patching /usr/lib/sagemath/local/lib/R/modules/internet.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/scipy/integrate/_quadpack.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/libs/ntl/ntl_GF2E.so
patching /usr/lib/sagemath/local/share/terminfo/n/news-o
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.groups.perm_gps.partn_ref.refinement_matrices
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.groups.perm_gps.partn_ref.refinement_matrices
patching /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.number_field.totallyreal_data
not found /usr/lib/sagemath/src/build/cython_debug/cython_debug_info_sage.rings.number_field.totallyreal_data
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/cvxopt/gsl.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/Twisted-15.5.0-py2.7-linux-x86_64.egg/twisted/python/_sendmsg.so
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/misc/constant_function.so
patching /usr/lib/sagemath/src/build/cythonized/sage/symbolic/expression.cpp
not found /usr/lib/sagemath/src/build/cythonized/sage/symbolic/expression.cpp
patching /usr/lib/sagemath/local/lib/python2.7/site-packages/sage/ext/pselect.so
patching /usr/lib/sagemath/local/lib/libstdc++.so.6.0.20
* AIMS PPA: relocate-once.py finished running. Ignore above Exception
sys:1: RuntimeWarning: not adding directory '' to sys.path since it's not owned by a trusted user.
Untrusted users could put files in this directory which might then be imported by your Python code. As a general precaution from similar exploits, you should not execute Python code from this directory
┌────────────────────────────────────────────────────────────────────┐
│ SageMath Version 7.0, Release Date: 2016-01-19                     │
│ Type "notebook()" for the browser-based notebook interface.        │
│ Type "help()" for help.                                            │
└────────────────────────────────────────────────────────────────────┘
Setting permissions of DOT_SAGE directory so only you can read and write it.
sage: quit()
Exiting Sage (CPU time 0m0.14s, Wall time 1m30.67s).

package information

Package: sagemath-upstream-binary
Versions: 
7.0~aimsppa1~qa201602031255151 (/var/lib/apt/lists/ppa.launchpad.net_aims_sagemath_ubuntu_dists_trusty_main_binary-amd64_Packages) (/var/lib/dpkg/status)
 Description Language: 
                 File: /var/lib/apt/lists/ppa.launchpad.net_aims_sagemath_ubuntu_dists_trusty_main_binary-amd64_Packages
                  MD5: 0a4e6e212377f9056703508d29d73269
 Description Language: en
                 File: /var/lib/apt/lists/ppa.launchpad.net_aims_sagemath_ubuntu_dists_trusty_main_i18n_Translation-en
                  MD5: 0a4e6e212377f9056703508d29d73269


Reverse Depends: 
  sagemath-upstream-binary-full:i386,sagemath-upstream-binary 6.8
  sagemath-upstream-binary:i386,sagemath-upstream-binary
  sagemath-upstream-binary-full,sagemath-upstream-binary 6.8
  sagemath-upstream-binary-full,sagemath-upstream-binary
Dependencies: 
7.0~aimsppa1~qa201602031255151 - libc6 (0 (null)) libexpat1 (0 (null)) libfontconfig1 (0 (null)) libgcc1 (0 (null)) libssl1.0.0 (0 (null)) libstdc++6 (0 (null)) libgfortran3 (0 (null)) libgomp1 (0 (null)) libquadmath0 (0 (null)) dpkg (2 1.15.6~) build-essential (0 (null)) gfortran (0 (null)) imagemagick (0 (null)) dvipng (0 (null)) texlive (0 (null)) texlive-pictures (0 (null)) icedtea-plugin (0 (null)) bash (0 (null)) python (0 (null)) sagemath-upstream-binary:i386 (0 (null)) 
Provides: 
7.0~aimsppa1~qa201602031255151 - 
Reverse Provides: 

relocate-once.py

#!/usr/bin/env python
"""
Rewrite Paths

This script can be used exactly once to move the directory to a
different location.
"""

import os
import os.path

ROOT_PATH = os.path.abspath(os.path.dirname(__file__))



class FilePatch(object):

    def __init__(self, search_and_replace, filename):
        self.search = search_and_replace.search
        self.replace = search_and_replace.replace
        self.filename = filename

	if os.path.isfile(self.filename):
		self.skip = False

        	self.st = os.stat(filename)
	        with open(self.filename, 'rb') as f:
	            self.content = f.read()
	else:
		self.content = ""
		self.skip = True
		print "not found {0}".format(self.filename)

    def substitute(self):
        """
        Perform the string substitution, changing the file length
        """
	if not self.skip:
	        self.content = self.content.replace(self.search, self.replace)

        return self
        
    def patch(self, start, end):
        """
        Perfom substitution in a fixed-size region of the file

        The file length is unchanged; If necessary the region is zero
        padded.

        Args:
            start(int): The start position of the string to replace
            end(int): The position of the terminating null
        """
	if self.skip:
		return self

        assert self.content[end:end+1] == b'\0'
        region = self.content[start:end]
        substituted = region.replace(self.search, self.replace)
        substituted+= b'\0' * (end - start - len(substituted))
        self.content = self.content[:start] + substituted + self.content[end:]
        return self

    def save(self):
	if self.skip:
		return

        with open(self.filename, 'wb') as f:
            f.write(self.content)
        os.utime(self.filename, (self.st.st_atime, self.st.st_mtime))

        
        
class SearchAndReplace(object):

    def __init__(self, search, replace):
        self.search = search.encode('utf-8')
        self.replace = replace.encode('utf-8')
        if len(self.search) < len(self.replace):
            raise RuntimeError(
                'path can be at most {0} characters long, but {1} has {2} characters'.format(
                    len(self.search), self.replace, len(self.replace)))

    def __call__(self, filename):
        filename = os.path.join(self.replace, filename)
        print('patching {0}'.format(filename))
        return FilePatch(self, filename)
    


        
        
print("""
Rewriting paths for your new installation directory
===================================================

This might take a few minutes but only has to be done once.
""")
        
p = SearchAndReplace('/mnt/highperf/buildbot/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma', ROOT_PATH)

p('src/build/cythonized/sage/rings/real_arb.c').substitute().save()
p('local/bin/dbmsr.so').patch(2815, 2925).patch(43426, 43579).patch(44761, 44914).patch(44963, 45087).patch(47854, 48019).save()
p('local/lib/python2.7/site-packages/sage/matrix/misc.so').patch(6825, 6935).patch(129328, 129468).patch(147392, 147517).patch(266682, 266822).patch(268472, 268605).patch(268606, 268746).patch(268747, 268870).patch(268871, 269024).patch(269073, 269197).patch(269198, 269312).patch(269313, 269433).patch(269434, 269553).patch(269554, 269672).patch(269673, 269787).patch(310453, 310557).patch(311850, 311990).save()
p('local/lib/python2.7/site-packages/sage/rings/real_lazy.so').patch(9493, 9603).patch(216696, 216840).patch(280896, 281025).patch(526903, 527047).patch(528670, 528802).patch(528803, 528917).patch(528918, 529071).patch(529154, 529278).patch(584203, 584347).patch(605367, 605471).save()
p('local/lib/python2.7/site-packages/sage/structure/parent.so').patch(8875, 8985).patch(304976, 305121).patch(396672, 396802).patch(691892, 692037).patch(693765, 693901).patch(693902, 694042).patch(694043, 694157).patch(694158, 694311).patch(694394, 694518).patch(694519, 694642).patch(791336, 791481).patch(794140, 794244).save()
p('local/include/atlas/atlas_dsyr_L2.h').substitute().save()
…

system information

$ uname -a
Linux xxxx-X550CC 3.13.0-77-generic #121-Ubuntu SMP Wed Jan 20 10:50:42 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
xxxx@xxxx-X550CC:~$ cat /etc/lsb-release 
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=14.04
DISTRIB_CODENAME=trusty
DISTRIB_DESCRIPTION="Ubuntu 14.04.3 LTS"