ASKSAGE: Sage Q&A Forum - RSS feedhttps://ask.sagemath.org/questions/Q&A Forum for SageenCopyright Sage, 2010. Some rights reserved under creative commons license.Sat, 30 Jul 2022 16:16:02 +0200Compile from source fails on Ubuntuhttps://ask.sagemath.org/question/63459/compile-from-source-fails-on-ubuntu/ I tried to compile sage from source. I did
git clone github.com/sagemath/sage.git /math/sage
cd /math/sage
make configure
./configure --enable-editable
make -j4
,but it didn't complete, returning after ~30minutes the following error :
[sagelib-9.7.beta6] error: subprocess-exited-with-error
[sagelib-9.7.beta6]
[sagelib-9.7.beta6] × python setup.py develop did not run successfully.
[sagelib-9.7.beta6] │ exit code: 1
[sagelib-9.7.beta6] ╰─> See above for output.
[sagelib-9.7.beta6]
[sagelib-9.7.beta6] note: This error originates from a subprocess, and is likely not a problem with pip.
[sagelib-9.7.beta6] full command: /math/sage/local/var/lib/sage/venv-python3.10/bin/python3 -c '
[sagelib-9.7.beta6] exec(compile('"'"''"'"''"'"'
[sagelib-9.7.beta6] # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
[sagelib-9.7.beta6] #
[sagelib-9.7.beta6] # - It imports setuptools before invoking setup.py, to enable projects that directly
[sagelib-9.7.beta6] # import from `distutils.core` to work with newer packaging standards.
[sagelib-9.7.beta6] # - It provides a clear error message when setuptools is not installed.
[sagelib-9.7.beta6] # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
[sagelib-9.7.beta6] # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
[sagelib-9.7.beta6] # manifest_maker: standard file '"'"'-c'"'"' not found".
[sagelib-9.7.beta6] # - It generates a shim setup.py, for handling setup.cfg-only projects.
[sagelib-9.7.beta6] import os, sys, tokenize
[sagelib-9.7.beta6]
[sagelib-9.7.beta6] try:
[sagelib-9.7.beta6] import setuptools
[sagelib-9.7.beta6] except ImportError as error:
[sagelib-9.7.beta6] print(
[sagelib-9.7.beta6] "ERROR: Can not execute `setup.py` since setuptools is not available in "
[sagelib-9.7.beta6] "the build environment.",
[sagelib-9.7.beta6] file=sys.stderr,
[sagelib-9.7.beta6] )
[sagelib-9.7.beta6] sys.exit(1)
[sagelib-9.7.beta6]
[sagelib-9.7.beta6] __file__ = %r
[sagelib-9.7.beta6] sys.argv[0] = __file__
[sagelib-9.7.beta6]
[sagelib-9.7.beta6] if os.path.exists(__file__):
[sagelib-9.7.beta6] filename = __file__
[sagelib-9.7.beta6] with tokenize.open(__file__) as f:
[sagelib-9.7.beta6] setup_py_code = f.read()
[sagelib-9.7.beta6] else:
[sagelib-9.7.beta6] filename = "<auto-generated setuptools caller>"
[sagelib-9.7.beta6] setup_py_code = "from setuptools import setup; setup()"
[sagelib-9.7.beta6]
[sagelib-9.7.beta6] exec(compile(setup_py_code, filename, "exec"))
[sagelib-9.7.beta6] '"'"''"'"''"'"' % ('"'"'/math/sage/src/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' --no-user-cfg develop --no-deps
[sagelib-9.7.beta6] cwd: /math/sage/src/
[sagelib-9.7.beta6] error: subprocess-exited-with-error
[sagelib-9.7.beta6]
[sagelib-9.7.beta6] × python setup.py develop did not run successfully.
[sagelib-9.7.beta6] │ exit code: 1
[sagelib-9.7.beta6] ╰─> See above for output.
[sagelib-9.7.beta6]
[sagelib-9.7.beta6] note: This error originates from a subprocess, and is likely not a problem with pip.
[sagelib-9.7.beta6]
[sagelib-9.7.beta6] real 0m25,129s
[sagelib-9.7.beta6] user 0m22,528s
[sagelib-9.7.beta6] sys 0m2,610s
make[4]: *** [Makefile:3002 : sagelib-SAGE_VENV-no-deps] Erreur 1
make[3]: *** [Makefile:3002 : /math/sage/local/var/lib/sage/venv-python3.10/var/lib/sage/installed/sagelib-9.7.beta6] Erreur 2
make[2]: *** [Makefile:2561 : all-start] Erreur 2
make[2] : on quitte le répertoire « /math/sage/build/make »
real 0m25,475s
user 0m22,867s
sys 0m2,665s
***************************************************************
Error building Sage.
The following package(s) may have failed to build (not necessarily
during this run of 'make all-start'):
It is safe to delete any log files and build directories, but they
contain information that is helpful for debugging build problems.
WARNING: If you now run 'make' again, the build directory of the
same version of the package will, by default, be deleted. Set the
environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.
make[1]: *** [Makefile:40 : all-start] Erreur 1
make[1] : on quitte le répertoire « /math/sage »
make: *** [Makefile:13 : all] Erreur 2
enter code here
I don't know what to do, I tried several times, it never complete.
Thank you for any helpjohnsmokeSat, 30 Jul 2022 16:16:02 +0200https://ask.sagemath.org/question/63459/Where to Set the environment variable SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent make from removing what has built so far?https://ask.sagemath.org/question/44397/where-to-set-the-environment-variable-sage_keep_built_spkgs-to-yes-to-prevent-make-from-removing-what-has-built-so-far/I am building sage-8.4 on a RPI3B running Raspbian Stretch and it gets stuck in the documentation compiling section https://pastebin.com/gysZzgW3 and if I terminate and redo the process with `make -j4` as before then it says
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.
Makefile:31: recipe for target 'all-start' failed
make[1]: *** [all-start] Error 1
make[1]: Leaving directory '/home/pi/sage-8.4'
Makefile:13: recipe for target 'all' failed
make: *** [all] Error 2
So I have been able to avoid the above message by doing
$ ln -sf /usr/lib/arm-linux-gnueabihf/libstdc++.so.6.22 /home/pi/sage-8.4/local/lib/libstdc++.so.6
but then again if I redo the make process, the docs built so far removed and the process starts from beginning of documentation building.
So how do I do this? Will just putting `export SAGE_KEEP_BUILT_SPKGS=yes` in `sage-8.4/src/bin/save-env-config` suffice and if it does then how to achieve it? so far I failed to make it work.pavelsayekatFri, 23 Nov 2018 21:26:46 +0100https://ask.sagemath.org/question/44397/Disable modules at compile-time or runtimehttps://ask.sagemath.org/question/43878/disable-modules-at-compile-time-or-runtime/ I'm building SAGE for a humble Raspberry Pi platform (although I'm currently experimenting compilation on a good computer), and given the power of the Pi target I'd like to build and use only a reduced part of SageMath's modules. Anything too far above the level of a high-school student can be cut off, I only plan to use exact calculus and basic analysis tools.
So far I've looked at the installation guide and tried a few things with the configure script, but I found no option to disable modules.
Is there anything planned for this purpose? Or do I have to build SageMath entirely no matter what?
I considered loading only part of the Python modules at runtime, but I figure SageMath will load the others when it sees fit.
Is there a way to disable part of SageMath at runtime?LepheMon, 08 Oct 2018 22:07:28 +0200https://ask.sagemath.org/question/43878/Linking a new libraryhttps://ask.sagemath.org/question/37612/linking-a-new-library/I'm trying to understand more about how Sage manages the software that it links to, so I can understand if I would like to pursue linking my software to it.
1. I have GPLv3 code. Is this license acceptable?
2. My software is written in C++. Do I do the builds or does somebody in an official Sage capacity do the build? How do I manage which compiler is used?
2. As a young researcher, it's important for me that people use my software and cite it. When I have used Sage in papers, in addition to citing Sage, I also cite the major libraries that Sage uses. How can I be confident that others will cite my software, and not just the Sage project?
If there is a source that answer these questions, I haven't found it yet, and I would be grateful for being pointed in the correct direction. Thanks!SageFanThu, 18 May 2017 00:46:10 +0200https://ask.sagemath.org/question/37612/Code stopped compiling out of nowhere for no apparent reasonhttps://ask.sagemath.org/question/30649/code-stopped-compiling-out-of-nowhere-for-no-apparent-reason/ Sage has all of a sudden stopped compiling my code. It happened seemingly out of nowhere and im getting very worried because i spent ALOT of time writing an algorithm. Basically nothing happens when i run the code the long grey line comes up with a green bar flashing and the normal output rectangle but it jsut stays in that state permanently. Nothing seems to fix the problem, i've tried going back in the history, copying and pasting to a new folder and worksheet changing the code, trying to get literally anything to compile but to no avail. Im literally dumbfounded at the moment.
EDIT: The green loading bar actually seems to be appearing at the top of the code when i try to compile. Also, I dont know if length is ever an issue with Sage Math worksheets but my code is 235 lines if that helps at all.
EDIT 2: I am using SageMathCloud via. the link on sagemath.org, my web browser is google chrome, the code is written in a SageMath Worksheet, just in case my OS is Windows 10, here is a link to the code itself [Problematic Code](http://pastebin.com/8A02NJau).lolWhoCaresThu, 12 Nov 2015 01:50:03 +0100https://ask.sagemath.org/question/30649/Is there any way to suppress the extra white space from compiling in R?https://ask.sagemath.org/question/10876/is-there-any-way-to-suppress-the-extra-white-space-from-compiling-in-r/Whenever I compile my R code, I get a lot of extra white space that just clogs my worksheet. Is there any way to suppress this? (Without changing the code to be on the same line using semicolons.) I'm working in Sage Worksheets on the cloud.mysn57Wed, 05 Feb 2014 16:37:47 +0100https://ask.sagemath.org/question/10876/[SOLVED] installation from source on debian (kali)https://ask.sagemath.org/question/10651/solved-installation-from-source-on-debian-kali/Hello everyone,
I've just installed my new OS :
Linux kali 3.7-trunk-amd64 #1 SMP Debian 3.7.2-0+kali8 x86_64 GNU/Linux
But I got this errror when i do make inside the directory.
cd spkg && \
"../spkg/pipestatus" \
"env SAGE_PARALLEL_SPKG_BUILD='' ./install all 2>&1" \
"tee -a ../logs/install.log"
/bin/sh: 2: ../spkg/pipestatus: Permission denied
make: *** [build] Error 126
It just makes no sense for me ... :s
I've hesitated to post this on the google discussion , tell me if it is the wrong place.
Do not hesitate to tell me anything you would need, logs etc ...
Thank you
Nicolas
EDIT : I extracted the source in a mounted disk ( sdb1, called Data ) and i copied the unzipped files into my main disk , where the file system is . (into /home/nico )
SOLVED : Effectively, the fact i extracted on another drive was the mistake. At first, i tried to chmod +x pipestatus and there was another error so it lead me to this. Finally, i re dezipped directly on the main disk on my file system, and it is running normally. It is still unclear why that did not work before, because the disk where i unzipped had no "noexec" option but anyway ..
Thank you very much all !!!
NikkolasgWed, 23 Oct 2013 08:27:32 +0200https://ask.sagemath.org/question/10651/Error while integrate using algorithm='sympy' (bug)https://ask.sagemath.org/question/10370/error-while-integrate-using-algorithmsympy-bug/Hello!
I found next bug:
var('x, y')
integrate(y, y, 0, 8*log(x))
RuntimeError: ECL says: Error executing code in Maxima: defint: upper
limit of integration must be real; found 8*log(x)
Then I decided to use sympy:
var('x, y')
integrate(y, y, 0, 8*log(x), algorithm='sympy')
32*log(x)^2
Nice! But when I replaced 0 --> 0.5 (int --> real):
var('x, y')
integrate(y, y, 0.5, 8*log(x), algorithm='sympy')
AttributeError: 'sage.rings.real_mpfr.RealLiteral' object has no
attribute '_sympy_'
M.... I opened real_mpfr.pyx and added:
1314 def _sympy_(self):
1315 """
1316 Return sympy object.
1317 AUTHORS: #########################
1318 """
1319 import sympy
1320 return(sympy.symplify(float(self)))
(I added line numbers in my code above and remove authors informations (that is about me))
Then I tryed to load:
load('/home/andrei/Programs/Sage/sage-5.10/devel/sage/sage/rings/real_mpfr.pyx')
And there are many-many errors while compilling... Help me please!
Thanks.
AndreWinSun, 21 Jul 2013 13:15:59 +0200https://ask.sagemath.org/question/10370/Compiling sage on opensuse 12.3https://ask.sagemath.org/question/10047/compiling-sage-on-opensuse-123/Dear Sage support group,
I am trying to compile sage 5.8 on my newly installed opensuse 12.3. However, the install fails after checking my "build system type".
I've copy pasted the error message below. Any help would be greatly appreciated.
Best,
Simon
***********************************************
make[1]: Entering directory `/home/gonneman/Downloads/sage-5.8/spkg'
make base
make[2]: Entering directory `/home/gonneman/Downloads/sage-5.8/spkg'
/home/gonneman/Downloads/sage-5.8/spkg/pipestatus "base/prereq-1.1-install 2>&1" "tee -a /home/gonneman/Downloads/sage-5.8/spkg/logs/prereq-1.1.log"
Starting prerequisite check.
Machine: Linux loki.site 3.7.10-1.1-desktop #1 SMP PREEMPT Thu Feb 28 15:06:29 UTC 2013 (82d3f21) x86_64 x86_64 x86_64 GNU/Linux
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... Invalid configuration `x86_64-unknown-linux-': machine `x86_64-unknown-linux' not recognized
configure: error: /bin/sh ./config.sub x86_64-unknown-linux- failed
You do not have all of the prerequisites needed to build Sage
from source. See the errors above.
If you would like to try the build anyway (to help porting)
export the variable 'SAGE_PORT' to something non-empty.
make[2]: *** [installed/prereq-1.1] Error 1
make[2]: Leaving directory `/home/gonneman/Downloads/sage-5.8/spkg'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/gonneman/Downloads/sage-5.8/spkg'
GonnemanMon, 22 Apr 2013 03:05:50 +0200https://ask.sagemath.org/question/10047/Compiling problem after sudden shutdownhttps://ask.sagemath.org/question/9918/compiling-problem-after-sudden-shutdown/I was building Sage 5.7 on Ubuntu 12.04 from source, but my computer overheated and shut down immediately. When I try to resume the compiling process there is an error on libfplll-3.0.12.p3.AshtarBalynestrySat, 16 Mar 2013 00:31:31 +0100https://ask.sagemath.org/question/9918/compile TeX from Sagehttps://ask.sagemath.org/question/9165/compile-tex-from-sage/Hola!
I'm working on a program which should output the results of its computations in form of a typesetted document (ideally pdf from *pdflatex*).
I'm trying to perfrom the final presentation part via `view` function, however, that doesn't seem to be the most convenient way (since `view` is aimed at typesetting **LaTeX** formulas of elements of a list). A lot of *hidden code* (headers, turned on math modes etc.) are really unpleasent to get around.
I'm pondering about generating an explicit `.tex` source code file. How can I call TeX compiler from Sage? I.e. how to compile it automatically in an own program, similarly as `view` does it?)
ThanX in advance!
Sage 5.1
Kubuntu 12.04MathemageFri, 20 Jul 2012 09:00:23 +0200https://ask.sagemath.org/question/9165/Compiling Sage with multiple coreshttps://ask.sagemath.org/question/9093/compiling-sage-with-multiple-cores/Hi all,
I am compiling Sage 5.0.1 in Ubuntu 12.04
According to the book "Sage: Beginner's Guide" to compile with multiple cores one needs to export a variable MAKE. I did so
export MAKe="make -j7"
and everything went well until the Atlas-3 compilation started. While compiling this (which is painfully big) only 1 core is being used.
Is there a way to compile all the parts of sage with multiple processors?
Thanks
JuanPiTue, 19 Jun 2012 07:02:57 +0200https://ask.sagemath.org/question/9093/Error compiling 5.0: scipy-0.9.p1https://ask.sagemath.org/question/8981/error-compiling-50-scipy-09p1/When compliting the latest sources from the web-site I get:
Error installing package scipy-0.9.p1
What should I do (apart from getting the binaries)?
Here's the last ~100 lines of the build:
compile options: '-I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7 -c'
gcc: scipy/spatial/ckdtree.c
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from scipy/spatial/ckdtree.c:158:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
scipy/spatial/ckdtree.c: In function __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree___init__:
scipy/spatial/ckdtree.c:2033:14: warning: variable __pyx_bshape_0_inner_mins set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2032:14: warning: variable __pyx_bstride_0_inner_mins set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2030:14: warning: variable __pyx_bshape_1_inner_data set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2029:14: warning: variable __pyx_bshape_0_inner_data set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2028:14: warning: variable __pyx_bstride_1_inner_data set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2027:14: warning: variable __pyx_bstride_0_inner_data set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2025:14: warning: variable __pyx_bshape_0_inner_maxes set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2024:14: warning: variable __pyx_bstride_0_inner_maxes set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2022:14: warning: variable __pyx_bshape_0_inner_indices set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2021:14: warning: variable __pyx_bstride_0_inner_indices set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c: In function __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree___dealloc__:
scipy/spatial/ckdtree.c:3413:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
scipy/spatial/ckdtree.c: In function __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree_query:
scipy/spatial/ckdtree.c:4461:14: warning: variable __pyx_bshape_1_xx set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:4460:14: warning: variable __pyx_bshape_0_xx set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:4459:14: warning: variable __pyx_bstride_1_xx set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:4458:14: warning: variable __pyx_bstride_0_xx set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c: At top level:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1666:1: warning: _import_array defined but not used [-Wunused-function]
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:236:1: warning: _import_umath defined but not used [-Wunused-function]
scipy/spatial/ckdtree.c:2012:13: warning: __pyx_doc_5scipy_7spatial_7ckdtree_7cKDTree___init__ defined but not used [-Wunused-variable]
gcc -pthread -shared -L/home/boris/its/soft/sft/sage-5.0-x86_64/local/lib -shared build/temp.linux-x86_64-2.7/scipy/spatial/ckdtree.o -L/home/boris/its/soft/sft/sage-5.0-x86_64/local/lib -Lbuild/temp.linux-x86_64-2.7 -lpython2.7 -o build/lib.linux-x86_64-2.7/scipy/spatial/ckdtree.so
building 'scipy.spatial._distance_wrap' extension
compiling C sources
C compiler: gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
creating build/temp.linux-x86_64-2.7/scipy/spatial/src
compile options: '-I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7 -c'
gcc: scipy/spatial/src/distance_wrap.c
In file included from /home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7/Python.h:8:0,
from scipy/spatial/src/distance_wrap.c:39:
/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7/pyconfig.h:1155:0: warning: "_POSIX_C_SOURCE" redefined [enabled by default]
/usr/include/features.h:215:0: note: this is the location of the previous definition
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from scipy/spatial/src/distance_wrap.c:40:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
scipy/spatial/src/distance_wrap.c: In function pdist_weighted_minkowski_wrap:
scipy/spatial/src/distance_wrap.c:866:7: warning: assignment discards const qualifier from pointer target type [enabled by default]
gcc: scipy/spatial/src/distance.c
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from scipy/spatial/src/distance.c:37:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1666:1: warning: _import_array defined but not used [-Wunused-function]
gcc -pthread -shared -L/home/boris/its/soft/sft/sage-5.0-x86_64/local/lib -shared build/temp.linux-x86_64-2.7/scipy/spatial/src/distance_wrap.o build/temp.linux-x86_64-2.7/scipy/spatial/src/distance.o -L/home/boris/its/soft/sft/sage-5.0-x86_64/local/lib -Lbuild/temp.linux-x86_64-2.7 -lpython2.7 -o build/lib.linux-x86_64-2.7/scipy/spatial/_distance_wrap.so
building 'scipy.special._cephes' extension
compiling C sources
C compiler: gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
compile options: '-I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7 -c'
gcc: scipy/special/_cephesmodule.c
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from scipy/special/_cephesmodule.c:12:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
scipy/special/_cephesmodule.c: In function scipy_special_raise_warning:
scipy/special/_cephesmodule.c:1055:5: error: expected =, ,, ;, asm or __attribute__ before char
scipy/special/_cephesmodule.c:1062:5: error: __save__ undeclared (first use in this function)
scipy/special/_cephesmodule.c:1062:5: note: each undeclared identifier is reported only once for each function it appears in
scipy/special/_cephesmodule.c:1063:5: error: expected ; before PyErr_WarnEx
scipy/special/_cephesmodule.c:1065:1: error: expected ; before } token
scipy/special/_cephesmodule.c:1076:18: error: invalid storage class for function errprint_func
scipy/special/_cephesmodule.c:1091:3: error: initializer element is not constant
scipy/special/_cephesmodule.c:1091:3: error: (near initialization for methods[0].ml_meth)
scipy/special/_cephesmodule.c:1177:1: error: expected declaration or statement at end of input
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from scipy/special/_cephesmodule.c:12:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
scipy/special/_cephesmodule.c: In function scipy_special_raise_warning:
scipy/special/_cephesmodule.c:1055:5: error: expected =, ,, ;, asm or __attribute__ before char
scipy/special/_cephesmodule.c:1062:5: error: __save__ undeclared (first use in this function)
scipy/special/_cephesmodule.c:1062:5: note: each undeclared identifier is reported only once for each function it appears in
scipy/special/_cephesmodule.c:1063:5: error: expected ; before PyErr_WarnEx
scipy/special/_cephesmodule.c:1065:1: error: expected ; before } token
scipy/special/_cephesmodule.c:1076:18: error: invalid storage class for function errprint_func
scipy/special/_cephesmodule.c:1091:3: error: initializer element is not constant
scipy/special/_cephesmodule.c:1091:3: error: (near initialization for methods[0].ml_meth)
scipy/special/_cephesmodule.c:1177:1: error: expected declaration or statement at end of input
error: Command "gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7 -c scipy/special/_cephesmodule.c -o build/temp.linux-x86_64-2.7/scipy/special/_cephesmodule.o" failed with exit status 1
Error building scipy.
real 8m36.650s
user 7m51.421s
sys 0m22.869s
************************************************************************
Error installing package scipy-0.9.p1
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file
/home/boris/its/soft/sft/sage-5.0-x86_64/spkg/logs/scipy-0.9.p1.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/home/boris/its/soft/sft/sage-5.0-x86_64/spkg/build/scipy-0.9.p1 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 '/home/boris/its/soft/sft/sage-5.0-x86_64/spkg/build/scipy-0.9.p1' && '/home/boris/its/soft/sft/sage-5.0-x86_64/sage' -sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
make[1]: *** [installed/scipy-0.9.p1] Error 1
make[1]: Leaving directory `/home/boris/its/soft/sft/sage-5.0-x86_64/spkg'
real 202m39.727s
user 169m59.525s
sys 11m1.101s
Error building Sage.
I'm on Kubuntu 12.04, I have build several previous version of Sage on my machine. Actually the cited part of the log point to the locally installed numpy:
/home/boris/.local/lib/python2.7/site-packages/numpy
This is strange: why would Sage use my locally installed numpy, when he has its own? Also this might be the source of the issue - since I'm using latest NumPy/SciPy - and if Sage looks at them he might go mad.
**Edit**:
I made a clean user at my notebook, and have succedded in compiling sage there. Then I've `chown -R` the compiled sources, and moved them to my primary account. But sage wouldn't start:
./sage
----------------------------------------------------------------------
| Sage Version 5.0, Release Date: 2012-05-14 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/boris/its/soft/sft/sage-5.0-x86_64/local/bin/sage-ipython", line 18, in <module>
import IPython
File "/usr/lib/python2.7/dist-packages/IPython/__init__.py", line 46, in <module>
from .frontend.terminal.embed import embed
File "/usr/lib/python2.7/dist-packages/IPython/frontend/terminal/embed.py", line 37, in <module>
from IPython.frontend.terminal.ipapp import load_default_config
File "/usr/lib/python2.7/dist-packages/IPython/frontend/terminal/ipapp.py", line 38, in <module>
from IPython.core.completer import IPCompleter
File "/usr/lib/python2.7/dist-packages/IPython/core/completer.py", line 84, in <module>
from IPython.utils import generics
File "/usr/lib/python2.7/dist-packages/IPython/utils/generics.py", line 19, in <module>
from IPython.external.simplegeneric import generic
File "/usr/lib/python2.7/dist-packages/IPython/external/simplegeneric/__init__.py", line 4, in <module>
from _simplegeneric import *
ImportError: No module named _simplegeneric
So it starts my system-wide ipython, instead of its own. ???
I tried
./sage -sh
./sage
but no effect. I also renamed previous .sage and .ipython folders - no effect.bk322Sat, 19 May 2012 10:33:40 +0200https://ask.sagemath.org/question/8981/Manually compiled R segfaultshttps://ask.sagemath.org/question/8790/manually-compiled-r-segfaults/Hello,
My R crashes when I try to compile it manually. This is the output of `make` when trying to compile `sagemath` from scratch:
gcc -std=gnu99 -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/home/liori/sage/sage-4.8/l
e -L/home/liori/sage/sage-4.8/local/lib/ -march=nocona -O2 -fomit-frame-pointer -s -pipe -c md5.c -o md5.o
gcc -std=gnu99 -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/home/liori/sage/sage-4.8/l
e -L/home/liori/sage/sage-4.8/local/lib/ -march=nocona -O2 -fomit-frame-pointer -s -pipe -c signals.c -o signals.o
gcc -std=gnu99 -shared -L/home/liori/sage/sage-4.8/local/lib/ -o tools.so text.o init.o Rmd5.o md5.o signals.o -L../../../../li
make[8]: Entering directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools/src'
make[8]: `Makedeps' is up to date.
make[8]: Leaving directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools/src'
make[8]: Entering directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools/src'
mkdir -p -- ../../../../library/tools/libs
make[8]: Leaving directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools/src'
make[7]: Leaving directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools/src'
make[6]: Leaving directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools'
*** caught segfault ***
address 0x7fff17a1f090, cause 'memory not mapped'
aborting ...
/bin/bash: line 1: 9951 Done echo "tools:::.install_package_description('.', '"../../../library/tools"')"
9952 Segmentation fault | R_DEFAULT_PACKAGES=NULL ../../../bin/R --vanilla --slave > /dev/null
Same thing when I tried to use a binary `sagemath` distribution and just recompile R there using `./sage -f r`. When R is run as standalone binary, it crashes right after printing invitation text. I launched it with `.../R --debugger gdb` and printed backtrace:
[...]
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Program received signal SIGSEGV, Segmentation fault.
strchrnul () at ../sysdeps/x86_64/strchrnul.S:34
34 ../sysdeps/x86_64/strchrnul.S: No such file or directory.
in ../sysdeps/x86_64/strchrnul.S
Current language: auto
The current source language is "auto; currently asm".
(gdb) bt
#0 strchrnul () at ../sysdeps/x86_64/strchrnul.S:34
#1 0x00007ffff712cd2f in __find_specmb (s=0x7fffffff9a00, format=0x7ffffffff028 <Address 0x7ffffffff028 out of bounds>,
ap=0x7fffffffbb80) at printf-parse.h:99
#2 _IO_vfprintf_internal (s=0x7fffffff9a00, format=0x7ffffffff028 <Address 0x7ffffffff028 out of bounds>, ap=0x7fffffffbb80)
at vfprintf.c:1325
#3 0x00007ffff71524f2 in _IO_vsnprintf (string=0x7fffffff9b80 "", maxlen=<value optimized out>,
format=0x7ffffffff028 <Address 0x7ffffffff028 out of bounds>, args=0x7fffffffbb80) at vsnprintf.c:120
#4 0x00007ffff793671b in Rvsnprintf () from /home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/lib/libR.so
#5 0x00007ffff7939d5f in Rf_warning () from /home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/lib/libR.so
#6 0x00007ffff797bd9c in setup_Rmainloop () from /home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/lib/libR.so
#7 0x00007ffff797cff6 in Rf_mainloop () from /home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/lib/libR.so
#8 0x00000000004008b8 in main ()
#9 0x00007ffff7109c8d in __libc_start_main (main=<value optimized out>, argc=<value optimized out>,
ubp_av=<value optimized out>, init=<value optimized out>, fini=<value optimized out>, rtld_fini=<value optimized out>,
stack_end=0x7fffffffe398) at libc-start.c:228
#10 0x00000000004007d9 in _start ()
R works when I use the precompiled binary from `sagemath` binary distribution, but I need to recompile it because of [R plots](http://ask.sagemath.org/question/1231/sage-from-precompiled-package-r-plots). This is the newest spkg available (`r-2.14.0.p1`).
EDIT1: Machine data: Debian Squeeze amd64, a Xen VPS, 1GB of RAM + 2GB of SWAP, with barely 80MB used for apps when trying to launch `R` manually. This is probably an i7 3GHz machine, but Xen hides cpu info.
EDIT2: My CFLAGS were: `-march=native -O2 -fomit-frame-pointer -s -pipe`. When I tried to recompile it for debugging purposes with `CFLAGS="-march=native -O0 -g" ./sage -f r`, it magically started working correctly...lioriTue, 13 Mar 2012 17:24:05 +0100https://ask.sagemath.org/question/8790/Sage from precompiled package -- R plotshttps://ask.sagemath.org/question/8789/sage-from-precompiled-package-r-plots/Hello,
I installed Sage on my Debian Squeeze server using `sage-4.8-linux-64bit-ubuntu_10.04.3_lts-x86_64-Linux.tar.lzma` package. I wanted to use it mostly for R, and therefore tried some plotting, but I get the known `X11 is not available` message.
I installed packages recommended here in other questions, such as `xorg-dev`, `libpango1.0-dev` and `libcairo2-dev`, and restarted the worksheet, but with no results.
Do I need to recompile `sage` now?lioriTue, 13 Mar 2012 11:26:14 +0100https://ask.sagemath.org/question/8789/Notebook errors when compiling Sage from sourcehttps://ask.sagemath.org/question/8692/notebook-errors-when-compiling-sage-from-source/Hi, everyone. I've been using the Sage binary on Kubuntu 11.10 and decided to try compiling Sage for better R support. It compiled, but the notebook is not working properly -- it gives me no output. I type in commands, click on "evaluate," and nothing happens, regardless of what the command was. No confirmations, no graphs, no error messages, no nothing. The binary works, but not what I compiled from source.
My system is using the 3.0.0-12-generic kernel, and I have all the packages (build-essential, gfortran, M4, bison) mentioned in the installation guide. I made sure to explicitly set the path to gfortran (export SAGE_FORTRAN=/usr/bin/gfortran). I couldn't find libgfortran.so, however, so I couldn't set SAGE_FORTRAN_LIB.
Any suggestions? I appreciate the help given on my last question a while back, and am hoping the Sage community can field this one again.RubinThu, 02 Feb 2012 19:23:05 +0100https://ask.sagemath.org/question/8692/installing on ubuntu 11.04https://ask.sagemath.org/question/8252/installing-on-ubuntu-1104/sage download website doesn't have a pre-build version for ubuntu 11.04. do people just compile from source?kirill_igumMon, 01 Aug 2011 11:42:14 +0200https://ask.sagemath.org/question/8252/