needless to say you might want to check your Homebrew, perhaps installing more things.
there are now positively reviewed tickets that allow you to use, R, openblas, and gsl from homebrew. On Mon, 23 Dec 2019, 18:10 Dima Pasechnik, <[email protected]> wrote: > how about following the advice below and > > brew install pkg-config libpng > > > > On Mon, 23 Dec 2019, 17:04 David Roe, <[email protected]> wrote: > >> 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 >> <http://math.mit.edu/~roed/singular-4.1.1p2.p0.log> and matplotlib >> <http://math.mit.edu/~roed/matplotlib-2.2.4.p0.log> logs below, and >> posted config.log <http://math.mit.edu/~roed/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 [email protected] 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 >> >> On Sat, Dec 21, 2019 at 10:34 AM Clayton Cafiero <[email protected]> >> wrote: >> >>> Oh great. Thanks to both. I'll give this a try. >>> >>> >>> >>> On Saturday, December 21, 2019 at 10:40:34 AM UTC-5, Clayton Cafiero >>> wrote: >>>> >>>> macOS Catalina 10.15.2 (19C57) >>>> >>>> Tried downloading and installing binary >>>> (sage-8.9-OSX_10.14.6-x86_64.dmg) but when run macOS complained bitterly >>>> about every file Sage tried to load when starting with >>>> >>>> “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. >>>> >>>> % xcodebuild -version >>>> Xcode 11.2 >>>> Build version 11B52 >>>> >>>> Downloaded Sage 8.9 source from mirror. Followed instructions in >>>> README.md, specifically >>>> >>>> * __OS X:__ >>>> * Make sure you have installed the most recent version >>>> of Xcode which you can install for free from the App Store. >>>> * You also need to install the "command line tools". When >>>> using OS X Mavericks, after installing Xcode, run >>>> `xcode-select --install` from a terminal window: >>>> Then click "Install" in the pop-up window. >>>> When using OS X Mountain Lion or earlier, you need to install the >>>> command line tools from Xcode: run Xcode; then from the File >>>> menu, choose "Preferences", then the "Downloads" tab, and then >>>> "Install" the Command Line Tools. You might also have Homebrew or >>>> a similar "Apple's missing package manager" system installed, >>>> with >>>> and libraries such gfortran, gmp, etc installed. (However, this >>>> is still experimental as of May 2019). >>>> >>>> ... >>>> >>>> Extract the tarball >>>> >>>> tar zxvf sage-*.tar.gz >>>> >>>> cd into the Sage directory and type make >>>> >>>> cd sage-*/ >>>> make >>>> >>>> This ran for quite a while and then failed, informing me to >>>> check /Users/myname/Downloads/sage-8.9/logs/pkgs/gfortran-7.4.0.log for >>>> more information. This file has over 500k lines and ends with >>>> >>>> ../../../src/libssp/gets-chk.c:59:13: error: storage class specified >>>> for parameter '__chk_fail' >>>> extern void __chk_fail (void) __attribute__((__noreturn__)); >>>> ^~~~~~~~~~ >>>> ../../../src/libssp/gets-chk.c:63:1: error: expected '=', ',', ';', >>>> 'asm' or '__attribute__' before '{' token >>>> { >>>> ^ >>>> In file included from >>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/sys/wait.h:110:0, >>>> from >>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/stdlib.h:66, >>>> from ../../../src/libssp/gets-chk.c:39: >>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/sys/resource.h:447:9: >>>> error: old-style parameter declarations in prototyped function definition >>>> int getiopolicy_np(int, int) __OSX_AVAILABLE_STARTING(__MAC_10_5, >>>> __IPHONE_2_0); >>>> ^~~~~~~~~~~~~~ >>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/sys/resource.h:447:1: >>>> error: parameter name omitted >>>> int getiopolicy_np(int, int) __OSX_AVAILABLE_STARTING(__MAC_10_5, >>>> __IPHONE_2_0); >>>> ^~~ >>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/sys/resource.h:447:1: >>>> error: parameter name omitted >>>> ../../../src/libssp/gets-chk.c:92:1: error: expected '{' at end of input >>>> } >>>> ^ >>>> ../../../src/libssp/gets-chk.c:92:1: warning: control reaches end of >>>> non-void function [-Wreturn-type] >>>> } >>>> ^ >>>> make[7]: *** [gets-chk.lo] Error 1 >>>> make[6]: *** [all] Error 2 >>>> make[5]: *** [all-target-libssp] Error 2 >>>> make[4]: *** [all] Error 2 >>>> >>>> ************************************************************************************************ >>>> Error building gfortran-7.4.0 >>>> >>>> ************************************************************************************************ >>>> >>>> Zip of this complete file is attached. >>>> >>>> Any suggestions? Please advise. TYVVM. >>>> >>>> >>>> >>>> >>>> -- >>> 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 [email protected]. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/sage-devel/41b925a3-39f8-43fd-b946-839b81646286%40googlegroups.com >>> <https://groups.google.com/d/msgid/sage-devel/41b925a3-39f8-43fd-b946-839b81646286%40googlegroups.com?utm_medium=email&utm_source=footer> >>> . >>> >> -- >> 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 [email protected]. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/sage-devel/CAChs6_mSVv0jVPKdLLjwN3yCX%3DP4dSXKFVMFrCr1D93aWp%2Bmvw%40mail.gmail.com >> <https://groups.google.com/d/msgid/sage-devel/CAChs6_mSVv0jVPKdLLjwN3yCX%3DP4dSXKFVMFrCr1D93aWp%2Bmvw%40mail.gmail.com?utm_medium=email&utm_source=footer> >> . >> > -- 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAAWYfq0%3DqpFrGLtN8ffYA86c%2BRrXV1DZqP1VwVvZZDMcPsOQxg%40mail.gmail.com.
