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2020-02-14 22:32:26 -0500 commented question Sage 9.0 build fails at the sagelib step

Thank you for your reply. The root cause appears to be some patches that was applying to it that I thought were necessary but turns out weren't needed. In addition, the SlackBuilds script looks like it was updated recently to account for the failure in building the documentation. Either way, I got it to build now!

2020-02-14 09:33:22 -0500 asked a question Sage 9.0 build fails at the sagelib step

Hi,

I was hoping that someone would help me figure out why my build keeps failing. The last few lines before it failed was

[493/500] gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -fPIC -I./sage/libs/pynac -I./sage/cpython -Isage/libs/pynac -Isage/cpython -I/opt/sage/local/lib/python3.7/site-packages/cysignals -I/opt/sage/local/include -I/opt/sage/src -I/opt/sage/src/sage/ext -I/opt/sage/local/include/python3.7m -I/opt/sage/local/lib/python3.7/site-packages/numpy/core/include -Ibuild/cythonized -I/opt/sage/local/include/python3.7m -c build/cythonized/sage/symbolic/expression.cpp -o build/temp.linux-x86_64-3.7/build/cythonized/sage/symbolic/expression.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -std=c++11 -DSING_NDEBUG -DOM_NDEBUG -I/opt/sage/local/include/singular -I/opt/sage/local/include/
In file included from /opt/sage/local/include/pynac/lst.h:26,
                from /opt/sage/local/include/pynac/ginac.h:37,
                from ./sage/libs/pynac/pynac_wrap.h:13,
                from build/cythonized/sage/symbolic/expression.cpp:677:
/opt/sage/local/include/pynac/container.h: In member function :
/opt/sage/local/include/pynac/container.h:592:3: warning: this  clause does not guard... [-Wmisleading-indentation]
 592 |   if (is_a<container<C> >(result))
     |   ^~
/opt/sage/local/include/pynac/container.h:595:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 
 595 |    return result;
     |    ^~~~~~
/opt/sage/local/include/pynac/container.h:597:3: warning: this  clause does not guard... [-Wmisleading-indentation]
 597 |   if (is_a<container<C> >(*this))
     |   ^~
/opt/sage/local/include/pynac/container.h:600:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 
 600 |    return *this;
     |    ^~~~~~
/opt/sage/local/include/pynac/container.h: In instantiation of :
/opt/sage/local/include/pynac/container.h:589:29:   required from 
/opt/sage/local/include/pynac/container.h:579:4:   required from here
/opt/sage/local/include/pynac/container.h:803:22: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move]
 803 |    return std::move(s);
     |                      ^
/opt/sage/local/include/pynac/container.h:803:22: note: remove  call
g++ -pthread -shared -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib -L. -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib build/temp.linux-x86_64-3.7/build/cythonized/sage/symbolic/expression.o -L/opt/sage/local/lib -L/opt/sage/local/lib -lgmp -lpynac -lstdc++ -lpython3.7m -o build/lib.linux-x86_64-3.7/sage/symbolic/expression.cpython-37m-x86_64-linux-gnu.so -lpari
[494/500] gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -fPIC -I./sage/cpython -Isage/cpython -I./sage/libs/ntl -I./sage/libs/pynac -Isage/libs/pynac -I/opt/sage/local/include -I/opt/sage/src -I/opt/sage/src/sage/ext -I/opt/sage/local/include/python3.7m -I/opt/sage/local/lib/python3.7/site-packages/numpy/core/include -Ibuild/cythonized -I/opt/sage/local/include/python3.7m -c build/cythonized/sage/symbolic/function.cpp -o build/temp.linux-x86_64-3.7/build/cythonized/sage/symbolic/function.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -std=c++11 -DSING_NDEBUG -DOM_NDEBUG -I/opt/sage/local/include/singular -I/opt/sage/local/include/
In file included from /opt/sage/local/include/pynac/lst.h:26,
                from /opt/sage/local/include/pynac/ginac.h:37,
                from ./sage/libs/pynac/pynac_wrap.h:13,
                from build/cythonized/sage/symbolic/function.cpp:674:
/opt/sage/local/include/pynac/container.h: In member function :
/opt/sage/local/include/pynac/container.h:592:3: warning: this  clause does not guard... [-Wmisleading-indentation]
 592 |   if (is_a<container<C> >(result))
     |   ^~
/opt/sage/local/include/pynac/container.h:595:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 
 595 |    return result;
     |    ^~~~~~
/opt/sage/local/include/pynac/container.h:597:3: warning: this  clause does not guard... [-Wmisleading-indentation]
 597 |   if (is_a<container<C> >(*this))
     |   ^~
/opt/sage/local/include/pynac/container.h:600:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 
 600 |    return *this;
     |    ^~~~~~
/opt/sage/local/include/pynac/container.h: In instantiation of :
/opt/sage/local/include/pynac/container.h:589:29:   required from 
/opt/sage/local/include/pynac/container.h:579:4:   required from here
/opt/sage/local/include/pynac/container.h:803:22: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move]
 803 |    return std::move(s);
     |                      ^
/opt/sage/local/include/pynac/container.h:803:22: note: remove  call
g++ -pthread -shared -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib -L. -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib build/temp.linux-x86_64-3.7/build/cythonized/sage/symbolic/function.o -L/opt/sage/local/lib -L/opt/sage/local/lib -lgmp -lpynac -lstdc++ -lpython3.7m -o build/lib.linux-x86_64-3.7/sage/symbolic/function.cpython-37m-x86_64-linux-gnu.so
[495/500] gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -fPIC -I./sage/libs/pynac -I./sage/cpython -Isage/libs/pynac -Isage/cpython -I/opt/sage/local/include -I/opt/sage/src -I/opt/sage/src/sage/ext -I/opt/sage/local/include/python3.7m -I/opt/sage/local/lib/python3.7/site-packages/numpy/core/include -Ibuild/cythonized -I/opt/sage/local/include/python3.7m -c build/cythonized/sage/symbolic/getitem.cpp -o build/temp.linux-x86_64-3.7/build/cythonized/sage/symbolic/getitem.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -std=c++11 -DSING_NDEBUG -DOM_NDEBUG -I/opt/sage/local/include/singular -I/opt/sage/local/include/
In file included from /opt/sage/local/include/pynac/lst.h:26,
                from /opt/sage/local/include/pynac/ginac.h:37,
                from ./sage/libs/pynac/pynac_wrap.h:13,
                from build/cythonized/sage/symbolic/getitem.cpp:670:
/opt/sage/local/include/pynac/container.h: In member function :
/opt/sage/local/include/pynac/container.h:592:3: warning: this  clause does not guard... [-Wmisleading-indentation]
 592 |   if (is_a<container<C> >(result))
     |   ^~
/opt/sage/local/include/pynac/container.h:595:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 
 595 |    return result;
     |    ^~~~~~
/opt/sage/local/include/pynac/container.h:597:3: warning: this  clause does not guard... [-Wmisleading-indentation]
 597 |   if (is_a<container<C> >(*this))
     |   ^~
/opt/sage/local/include/pynac/container.h:600:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 
 600 |    return *this;
     |    ^~~~~~
/opt/sage/local/include/pynac/container.h: In instantiation of :
/opt/sage/local/include/pynac/container.h:589:29:   required from 
/opt/sage/local/include/pynac/container.h:579:4:   required from here
/opt/sage/local/include/pynac/container.h:803:22: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move]
 803 |    return std::move(s);
     |                      ^
/opt/sage/local/include/pynac/container.h:803:22: note: remove  call
g++ -pthread -shared -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib -L. -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib build/temp.linux-x86_64-3.7/build/cythonized/sage/symbolic/getitem.o -L/opt/sage/local/lib -L/opt/sage/local/lib -lgmp -lpynac -lstdc++ -lpython3.7m -o build/lib.linux-x86_64-3.7/sage/symbolic/getitem.cpython-37m-x86_64-linux-gnu.so
[496/500] gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -fPIC -I./sage/libs/pynac -I./sage/cpython -Isage/libs/pynac -Isage/cpython -I./sage/libs/ntl -I/opt/sage/local/lib/python3.7/site-packages/cypari2 -I/opt/sage/local/include -I/opt/sage/src -I/opt/sage/src/sage/ext -I/opt/sage/local/include/python3.7m -I/opt/sage/local/lib/python3.7/site-packages/numpy/core/include -Ibuild/cythonized -I/opt/sage/local/include/python3.7m -c build/cythonized/sage/symbolic/ring.cpp -o build/temp.linux-x86_64-3.7/build/cythonized/sage/symbolic/ring.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -std=c++11 -DSING_NDEBUG -DOM_NDEBUG -I/opt/sage/local/include/singular -I/opt/sage/local/include/
In file included from /opt/sage/local/include/pynac/lst.h:26,
                from /opt/sage/local/include/pynac/ginac.h:37,
                from ./sage/libs/pynac/pynac_wrap.h:13,
                from build/cythonized/sage/symbolic/ring.cpp:678:
/opt/sage/local/include/pynac/container.h: In instantiation of :
/opt/sage/local/include/pynac/container.h:589:29:   required from 
/opt/sage/local/include/pynac/container.h:579:4:   required from here
/opt/sage/local/include/pynac/container.h:803:22: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move]
 803 |    return std::move(s);
     |                      ^
/opt/sage/local/include/pynac/container.h:803:22: note: remove  call
g++ -pthread -shared -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib -L. -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib build/temp.linux-x86_64-3.7/build/cythonized/sage/symbolic/ring.o -L/opt/sage/local/lib -L/opt/sage/local/lib -lgmp -lpynac -lstdc++ -lpython3.7m -o build/lib.linux-x86_64-3.7/sage/symbolic/ring.cpython-37m-x86_64-linux-gnu.so
[497/500] gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -fPIC -I./sage/libs/pynac -I./sage/cpython -Isage/libs/pynac -Isage/cpython -I/opt/sage/local/include -I/opt/sage/src -I/opt/sage/src/sage/ext -I/opt/sage/local/include/python3.7m -I/opt/sage/local/lib/python3.7/site-packages/numpy/core/include -Ibuild/cythonized -I/opt/sage/local/include/python3.7m -c build/cythonized/sage/symbolic/series.cpp -o build/temp.linux-x86_64-3.7/build/cythonized/sage/symbolic/series.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -std=c++11 -DSING_NDEBUG -DOM_NDEBUG -I/opt/sage/local/include/singular -I/opt/sage/local/include/
In file included from /opt/sage/local/include/pynac/lst.h:26,
                from /opt/sage/local/include/pynac/ginac.h:37,
                from ./sage/libs/pynac/pynac_wrap.h:13,
                from build/cythonized/sage/symbolic/series.cpp:670:
/opt/sage/local/include/pynac/container.h: In member function :
/opt/sage/local/include/pynac/container.h:592:3: warning: this  clause does not guard... [-Wmisleading-indentation]
 592 |   if (is_a<container<C> >(result))
     |   ^~
/opt/sage/local/include/pynac/container.h:595:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 
 595 |    return result;
     |    ^~~~~~
/opt/sage/local/include/pynac/container.h:597:3: warning: this  clause does not guard... [-Wmisleading-indentation]
 597 |   if (is_a<container<C> >(*this))
     |   ^~
/opt/sage/local/include/pynac/container.h:600:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 
 600 |    return *this;
     |    ^~~~~~
/opt/sage/local/include/pynac/container.h: In instantiation of :
/opt/sage/local/include/pynac/container.h:589:29:   required from 
/opt/sage/local/include/pynac/container.h:579:4:   required from here
/opt/sage/local/include/pynac/container.h:803:22: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move]
 803 |    return std::move(s);
     |                      ^
/opt/sage/local/include/pynac/container.h:803:22: note: remove  call
g++ -pthread -shared -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib -L. -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib build/temp.linux-x86_64-3.7/build/cythonized/sage/symbolic/series.o -L/opt/sage/local/lib -L/opt/sage/local/lib -lgmp -lpynac -lstdc++ -lpython3.7m -o build/lib.linux-x86_64-3.7/sage/symbolic/series.cpython-37m-x86_64-linux-gnu.so
[498/500] gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -fPIC -I./sage/libs/pynac -I./sage/cpython -Isage/libs/pynac -Isage/cpython -I/opt/sage/local/include -I/opt/sage/src -I/opt/sage/src/sage/ext -I/opt/sage/local/include/python3.7m -I/opt/sage/local/lib/python3.7/site-packages/numpy/core/include -Ibuild/cythonized -I/opt/sage/local/include/python3.7m -c build/cythonized/sage/symbolic/substitution_map.cpp -o build/temp.linux-x86_64-3.7/build/cythonized/sage/symbolic/substitution_map.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -std=c++11 -DSING_NDEBUG -DOM_NDEBUG -I/opt/sage/local/include/singular -I/opt/sage/local/include/
In file included from /opt/sage/local/include/pynac/lst.h:26,
                from /opt/sage/local/include/pynac/ginac.h:37,
                from ./sage/libs/pynac/pynac_wrap.h:13,
                from build/cythonized/sage/symbolic/substitution_map.cpp:670:
/opt/sage/local/include/pynac/container.h: In member function :
/opt/sage/local/include/pynac/container.h:592:3: warning: this  clause does not guard... [-Wmisleading-indentation]
 592 |   if (is_a<container<C> >(result))
     |   ^~
/opt/sage/local/include/pynac/container.h:595:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 
 595 |    return result;
     |    ^~~~~~
/opt/sage/local/include/pynac/container.h:597:3: warning: this  clause does not guard... [-Wmisleading-indentation]
 597 |   if (is_a<container<C> >(*this))
     |   ^~
/opt/sage/local/include/pynac/container.h:600:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 
 600 |    return *this;
     |    ^~~~~~
/opt/sage/local/include/pynac/container.h: In instantiation of :
/opt/sage/local/include/pynac/container.h:589:29:   required from 
/opt/sage/local/include/pynac/container.h:579:4:   required from here
/opt/sage/local/include/pynac/container.h:803:22: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move]
 803 |    return std::move(s);
     |                      ^
/opt/sage/local/include/pynac/container.h:803:22: note: remove  call
g++ -pthread -shared -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib -L. -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib build/temp.linux-x86_64-3.7/build/cythonized/sage/symbolic/substitution_map.o -L/opt/sage/local/lib -L/opt/sage/local/lib -lgmp -lpynac -lstdc++ -lpython3.7m -o build/lib.linux-x86_64-3.7/sage/symbolic/substitution_map.cpython-37m-x86_64-linux-gnu.so
[499/500] creating build/temp.linux-x86_64-3.7/build/cythonized/sage/tests
gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -fPIC -I./sage/cpython -Isage/cpython -I./sage/libs/ntl -I/opt/sage/local/lib/python3.7/site-packages/cysignals -I/opt/sage/local/include -I/opt/sage/src -I/opt/sage/src/sage/ext -I/opt/sage/local/include/python3.7m -I/opt/sage/local/lib/python3.7/site-packages/numpy/core/include -Ibuild/cythonized -I/opt/sage/local/include/python3.7m -c build/cythonized/sage/tests/stl_vector.cpp -o build/temp.linux-x86_64-3.7/build/cythonized/sage/tests/stl_vector.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -std=c++11
build/cythonized/sage/tests/stl_vector.cpp: In function :
build/cythonized/sage/tests/stl_vector.cpp:2891:30: warning: comparison of integer expressions of different signedness:  and  {aka } [-Wsign-compare]
2891 |       __pyx_t_1 = (__pyx_v_i < __pyx_v_self->data->size());
     |                    ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -pthread -shared -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib -L. -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib build/temp.linux-x86_64-3.7/build/cythonized/sage/tests/stl_vector.o -L/opt/sage/local/lib -L/opt/sage/local/lib -lgmp -lstdc++ -lpython3.7m -o build/lib.linux-x86_64-3.7/sage/tests/stl_vector.cpython-37m-x86_64-linux-gnu.so -lpari
[500/500] gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -fPIC -I/opt/sage/local/include -I/opt/sage/src -I/opt/sage/src/sage/ext -I/opt/sage/local/include/python3.7m -I/opt/sage/local/lib/python3.7/site-packages/numpy/core/include -Ibuild/cythonized -I/opt/sage/local/include/python3.7m -c build/cythonized/sage/tests/cython.c -o build/temp.linux-x86_64-3.7/build/cythonized/sage/tests/cython.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -std=c99
gcc -pthread -shared -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib -L. -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib -L/opt/sage/local/lib -Wl,-rpath,/opt/sage/local/lib build/temp.linux-x86_64-3.7/build/cythonized/sage/tests/cython.o -L/opt/sage/local/lib -L/opt/sage/local/lib -lpython3.7m -o build/lib.linux-x86_64-3.7/sage/tests/cython.cpython-37m-x86_64-linux-gnu.so
error: command 'gcc' failed with exit status 1
make[4]: *** [Makefile:33: sage] Error 1
make[4]: Leaving directory '/opt/sage/src'

I'm trying to build it using the SlackBuilds script with the version number changed. I tried to attach the log file but I don't have enough karma yet.

Any help or insight will be greatly appreciated.

2020-02-13 15:17:55 -0500 asked a question Sage 9.0 fails to build

Hi,

My sage build for version 9.0 fails to build at the 'sagelib' step and it seems to be related to the GAP any pynac packages. I've attached the log for it so hopefully someone can help me figure out what's wrong with the build.

Oddly enough, I have no problem building sage 8.8.

2020-02-06 10:46:57 -0500 asked a question Sage notebook only runs when a browser is already open

I just installed sage 8.8 (it's not the newest sage, but it works for the most part) on my Linux machine and I had everything working at some point but the other day it isn't working as I'd expect it to be. When I do

$ sage -n jupyter --browser=firefox

in the terminal without Firefox opened, I get

┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 8.8, Release Date: 2019-06-26                     │
│ Using Python 2.7.15. Type "help()" for help.                       │
└────────────────────────────────────────────────────────────────────┘
Please wait while the Sage Jupyter Notebook server starts...
[I 09:42:16.791 NotebookApp] Using MathJax: nbextensions/mathjax/MathJax.js
[I 09:42:17.016 NotebookApp] The port 8888 is already in use, trying another port.
[I 09:42:17.016 NotebookApp] The port 8889 is already in use, trying another port.
[I 09:42:17.017 NotebookApp] The port 8890 is already in use, trying another port.
[I 09:42:17.017 NotebookApp] The port 8891 is already in use, trying another port.
[I 09:42:17.017 NotebookApp] The port 8892 is already in use, trying another port.
[I 09:42:17.023 NotebookApp] Serving notebooks from local directory: /home/user
[I 09:42:17.023 NotebookApp] The Jupyter Notebook is running at:
[I 09:42:17.024 NotebookApp] <local host>
[I 09:42:17.024 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 09:42:17.027 NotebookApp] 

    To access the notebook, open this file in a browser:
        <server file>
    Or copy and paste one of these URLs:
        <localhost>

(I don't have enough karma to actually post the links but "local host" is the link to the notebook and "server file" is the HTML file in "/var/run/user/.../nbserver-...-open.html") which seems fine but Firefox doesn't appear to be open. When I try to open another Firefox browser, I get a message saying that there is already another browser opened when there isn't and I would have to kill the Firefox processes in order to open it again. Interestingly, when I try the same command again with a browser already opened, a new tab with the sage notebook appears.

I get the feeling that the problem could be coming from my init.sage file but I'm not sure if that would be the case.

~/.sage/init.sage:
==================================
from sage.misc.viewer import viewer
viewer.browser('open -a /usr/bin/firefox')

My environment variable SAGE_BROWSER is set to firefox:

$ echo $SAGE_BROWSER 
firefox

If there's anything else that you'd like me to provide, let me know.