Sage 8.9 build fails on macOS Catalina
Clayton Cafiero
“python2.7” cannot be opened because the developer cannot be verified."
If I use System Preferences > Security & Privacy to allow python2.7, then another warning appears:
“libpython2.7.dylib” cannot be opened because the developer cannot be verified."
...I had patience for about the first 100 files (_locale.so, zlib.so, _collections.so, blah, blah, blah), then I threw in the towel and tried to build.
Any suggestions? Please advise. TYVVM.
Dima Pasechnik
http://doc.sagemath.org/html/en/installation/conda.html
(provided they already have it for MacOS 10.15 - they do for 10.14,
not sure about 10.15)
To build from source, you might be on your own, as Sage 8.9 did not
support 10.15 - after all it was released before MacOS 10.15 was
released.
You may have better luck with the latest beta, Sage 9.0.beta9.
In this case you might like to minimise the trouble by using tools
from Homebrew or a similar "missing package manager" - e.g.
then you'd already have gfortran available, you won't need to build it yourself.
HTH,
Dmitrii
> You received this message because you are subscribed to the Google Groups "sage-devel" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/49affd15-db6a-4014-939f-3a01ae524a77%40googlegroups.com.
Clayton Cafiero
> To unsubscribe from this group and stop receiving emails from it, send an email to sage-...@googlegroups.com.
Dima Pasechnik
>
> I'd like to be able to build packages for Sage (e.g., Conjecturing) and this doesn't work when installing with conda.
https://git.sagemath.org/sage.git/diff?id=a596dec9240295b25cd1b48c4092d7eef4d60aed
on https://trac.sagemath.org/ticket/28745 (which is, admittedly, work
in progress).
Then one should able to build packages etc.
> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/c54d1cd1-c3d4-48e4-a133-ceb2304e7506%40googlegroups.com.
Isuru Fernando
To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAAWYfq25XjcyBtKS0vnyi1fRcP0Km-75JQ9qxc9GghfD9LyfUg%40mail.gmail.com.
Clayton Cafiero
David Roe
Hi all,
I have a new laptop running OS X 10.15 and haven't been able to successfully build Sage 9.0.beta9 on it. I used Apple's Migration Assistant to move everything from my old laptop (which was running a much older version of OS X), so I wouldn't be surprised if there were some leftover settings that are interfering (my old versions of Sage actually still run). In particular, I'm confused at why python 2 paths are showing up below when I thought sage-9.0.beta9 uses python3 by default. Any suggestions for how to clean out my environment appropriately would be appreciated. I've reinstalled xcode, the command line tools and a few brew packages (though I haven't uninstalled+reinstalled Homebrew completely).
The build fails on singular and matplotlib, running with 8 cores (I've tried previously building with just one core, but didn't on the most recent attempt).
$ make distclean
$ CC=clang CXX=clang++ FC=gfortran ./configure
$ MAKE="make -j8" make build
I've included the ends of the singular and matplotlib logs below, and posted config.log.
/bin/bash ../../../libtool --tag=CXX --mode=link clang++ -std=gnu++11 -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -O2 -g -pipe -fno-common -g0 -O3 -Wno-unused-function -Wno-trigraphs -Wno-unused-parameter -Wunknown-pragmas -Wno-unused-variable -fomit-frame-pointer -fwrapv -fvisibility=default -finline-functions -fno-exceptions -fno-threadsafe-statics -funroll-loops -fno-delete-null-pointer-checks -fno-rtti -Qunused-arguments -isysroot /Developer/SDKs/MacOSX10.6.sdk -isysroot /Developer/SDKs/MacOSX10.6.sdk -g -F/Library/Frameworks -u _PyMac_Error Python.framework/Versions/2.7/Python -module -export-dynamic -avoid-version -flat_namespace -weak_reference_mismatches weak -undefined dynamic_lookup -L/Users/roed/sage/sage-9.0.beta9/local/lib -Wl,-rpath,/Users/roed/sage/sage-9.0.beta9/local/lib -pipe -fno-common -g0 -O3 -Wno-unused-function -Wno-trigraphs -Wno-unused-parameter -Wunknown-pragmas -Wno-unused-variable -fomit-frame-pointer -fwrapv -fvisibility=default -finline-functions -fno-exceptions -fno-threadsafe-statics -funroll-loops -fno-delete-null-pointer-checks -Qunused-arguments -rdynamic -flat_namespace -Wl,-bind_at_load -Wl,-undefined,dynamic_lookup -o pyobject.la -rpath /Users/roed/sage/sage-9.0.beta9/local/libexec/singular/MOD pyobject_la-pyobject.lo -isysroot /Developer/SDKs/MacOSX10.6.sdk -isysroot /Developer/SDKs/MacOSX10.6.sdk -g -F/Library/Frameworks -u _PyMac_Error Python.framework/Versions/2.7/Python -lreadline -lncurses -lmpfr
libtool: link: clang++ -std=gnu++11 -Wl,-undefined -Wl,dynamic_lookup -o .libs/pyobject.so -bundle .libs/pyobject_la-pyobject.o -L/Users/roed/sage/sage-9.0.beta9/local/lib -lreadline -lncurses -lmpfr -O2 -g -g0 -O3 -isysroot /Developer/SDKs/MacOSX10.6.sdk -isysroot /Developer/SDKs/MacOSX10.6.sdk -g -F/Library/Frameworks -Wl,-rpath -Wl,/Users/roed/sage/sage-9.0.beta9/local/lib -g0 -O3 -Wl,-bind_at_load -Wl,-undefined -Wl,dynamic_lookup -isysroot /Developer/SDKs/MacOSX10.6.sdk -isysroot /Developer/SDKs/MacOSX10.6.sdk -g -F/Library/Frameworks
clang: warning: no such sysroot directory: '/Developer/SDKs/MacOSX10.6.sdk' [-Wmissing-sysroot]
ld: library not found for -lncurses
clang: error: linker command failed with exit code 1 (use -v to see invocation)
BUILDING MATPLOTLIB
matplotlib: yes [2.2.4]
python: yes [3.7.3 (default, Dec 23 2019, 00:02:12) [Clang
11.0.0 (clang-1100.0.33.16)]]
platform: yes [darwin]
REQUIRED DEPENDENCIES AND EXTENSIONS
numpy: yes [version 1.16.1]
install_requires: yes [handled by setuptools]
libagg: yes [pkg-config information for 'libagg' could not
be found. Using local copy.]
freetype: yes [version 2.9.1]
png: no [The C/C++ header for libpng (png.h) could not
be found. You may need to install the development
package.]
qhull: yes [pkg-config information for 'libqhull' could not
be found. Using local copy.]
OPTIONAL SUBPACKAGES
sample_data: yes [installing]
toolkits: yes [installing]
OPTIONAL BACKEND EXTENSIONS
macosx: no [skipping due to configuration]
qt5agg: no [PySide2 not found; PyQt5 not found]
qt4agg: no [PySide not found; PyQt4 not found]
gtk3agg: no [Requires pygobject to be installed.]
gtk3cairo: no [Requires cairocffi or pycairo to be installed.]
gtkagg: no [skipping due to configuration]
tkagg: yes [installing; run-time loading from Python Tcl /
Tk]
wxagg: no [skipping due to configuration]
gtk: no [skipping due to configuration]
agg: yes [installing]
cairo: no [cairocffi or pycairo not found]
windowing: no [skipping due to configuration]
OPTIONAL LATEX DEPENDENCIES
dvipng: yes [version 1.15]
ghostscript: yes [version 9.19]
latex: yes [version 3.14159265]
pdftops: no
OPTIONAL PACKAGE DATA
dlls: no [skipping due to configuration]
============================================================================
* The following required packages can not be built:
* png
* Try installing png with `brew install libpng` and
* pkg-config with `brew install pkg-config`
Cleaning up...
Removing source in /private/var/folders/5z/00qw7rqx65qb3n_vn5_2ylxh0000gn/T/pip-req-build-1gyeljlc
Removed file:///Users/roed/sage/sage-9.0.beta9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/src from build tracker '/private/var/folders/5z/00qw7rqx65qb3n_vn5_2ylxh0000gn/T/pip-req-tracker-teeref1m'
Removed build tracker '/private/var/folders/5z/00qw7rqx65qb3n_vn5_2ylxh0000gn/T/pip-req-tracker-teeref1m'
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/5z/00qw7rqx65qb3n_vn5_2ylxh0000gn/T/pip-req-build-1gyeljlc/
Exception information:
Traceback (most recent call last):
File "/Users/roed/sage/sage-9.0.beta9/local/lib/python3.7/site-packages/pip/_internal/cli/base_command.py", line 143, in main
status = self.run(options, args)
File "/Users/roed/sage/sage-9.0.beta9/local/lib/python3.7/site-packages/pip/_internal/commands/install.py", line 318, in run
resolver.resolve(requirement_set)
File "/Users/roed/sage/sage-9.0.beta9/local/lib/python3.7/site-packages/pip/_internal/resolve.py", line 102, in resolve
self._resolve_one(requirement_set, req)
File "/Users/roed/sage/sage-9.0.beta9/local/lib/python3.7/site-packages/pip/_internal/resolve.py", line 256, in _resolve_one
abstract_dist = self._get_abstract_dist_for(req_to_install)
File "/Users/roed/sage/sage-9.0.beta9/local/lib/python3.7/site-packages/pip/_internal/resolve.py", line 209, in _get_abstract_dist_for
self.require_hashes
File "/Users/roed/sage/sage-9.0.beta9/local/lib/python3.7/site-packages/pip/_internal/operations/prepare.py", line 298, in prepare_linked_requirement
abstract_dist.prep_for_dist(finder, self.build_isolation)
File "/Users/roed/sage/sage-9.0.beta9/local/lib/python3.7/site-packages/pip/_internal/operations/prepare.py", line 126, in prep_for_dist
self.req.run_egg_info()
File "/Users/roed/sage/sage-9.0.beta9/local/lib/python3.7/site-packages/pip/_internal/req/req_install.py", line 473, in run_egg_info
command_desc='python setup.py egg_info')
File "/Users/roed/sage/sage-9.0.beta9/local/lib/python3.7/site-packages/pip/_internal/utils/misc.py", line 705, in call_subprocess
% (command_desc, proc.returncode, cwd))
pip._internal.exceptions.InstallationError: Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/5z/00qw7rqx65qb3n_vn5_2ylxh0000gn/T/pip-req-build-1gyeljlc/
Error: installing with pip3 failed
Here's some configuration information for my computer:
$ sw_vers
ProductName: Mac OS X
ProductVersion: 10.15.2
BuildVersion: 19C57
$ xcodebuild -version
Xcode 11.3
Build version 11C29
$ xcode-select --version
xcode-select version 2373.
$ brew list
autoconf gperftools libunistring python@2
automake icu4c mpfr readline
cloc isl nettle sqlite
emacs libdvdcss ninja sshuttle
freetype libevent node unbound
gcc libffi openssl wget
gdbm libidn2 openssl@1.1 xz
gettext libmpc p11-kit yasm
git libpng pcre2
gmp libtasn1 postgresql
gnutls libtool python
$ env
TMPDIR=/var/folders/5z/00qw7rqx65qb3n_vn5_2ylxh0000gn/T/
XPC_FLAGS=0x0
LaunchInstanceID=FA121E45-B0D4-4A9B-AC7B-3DA0BBD3E265
TERM=xterm-256color
LANG=en_US.UTF-8
SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.HSZ3ucXzaN/Listeners
SECURITYSESSIONID=186a8
XPC_SERVICE_NAME=0
TERM_PROGRAM=Apple_Terminal
TERM_PROGRAM_VERSION=433
TERM_SESSION_ID=AB48F780-8DBD-4585-84FF-E98A2E468EF9
SHELL=/bin/zsh
HOME=/Users/roed
LOGNAME=roed
USER=roed
PATH=/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Library/Frameworks/Mono.framework/Versions/Current/Commands
SHLVL=1
PWD=/Users/roed
OLDPWD=/Users/roed
EDITOR=emacs
SAGE_INSTALL_CCACHE=yes
_=/usr/bin/env
Thanks!
David
--
You received this message because you are subscribed to the Google Groups "sage-devel" group.
To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/41b925a3-39f8-43fd-b946-839b81646286%40googlegroups.com.
Dima Pasechnik
To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAChs6_mSVv0jVPKdLLjwN3yCX%3DP4dSXKFVMFrCr1D93aWp%2Bmvw%40mail.gmail.com.
Dima Pasechnik
Samuel Lelievre
that will allow to build the least possible number
of Sage components when building from source?
David, the reference to "MacOSX10.6.sdk" in this line:
