Hi, I recently tried adding openssl to the app.dmg prebuilt sage 9 binary via: sage -i openssl && sage -f python3. During the rebuild, rpy2 failed with the message:
[rpy2-2.8.2.p1] dyld: lazy symbol binding failed: Symbol not found: _timespec_get [rpy2-2.8.2.p1] Referenced from: /Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/R/lib/libR.dylib [rpy2-2.8.2.p1] Expected in: /usr/lib/libSystem.B.dylib [rpy2-2.8.2.p1] [rpy2-2.8.2.p1] dyld: Symbol not found: _timespec_get [rpy2-2.8.2.p1] Referenced from: /Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/R/lib/libR.dylib [rpy2-2.8.2.p1] Expected in: /usr/lib/libSystem.B.dylib From Googling, it appears that the problem might be tied to changes made by Xcode 11. I will try to downgrade to Xcode 10 to see if this fixes the problem. For what it's worth I am currently able to build sage from scratch, it's just that rebuilding is a problem. Thanks, Zach -- 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+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/7963f9e9-a8dd-4acf-a584-e8e078f456a4%40googlegroups.com.
Found local metadata for rpy2-2.8.2.p1 Attempting to download package rpy2-2.8.2.tar.gz from mirrors http://mirrors.mit.edu/sage/spkg/upstream/rpy2/rpy2-2.8.2.tar.gz [......................................................................] rpy2-2.8.2.p1 ==================================================== Setting up build directory for rpy2-2.8.2.p1 Finished extraction Applying patches from ../patches... Applying ../patches/cygwin.patch patching file rpy/rinterface/na_values.c patching file rpy/rinterface/_rinterface.c Hunk #1 succeeded at 1156 (offset -6 lines). Hunk #2 succeeded at 3750 (offset 1 line). Hunk #3 succeeded at 3760 (offset 1 line). Hunk #4 succeeded at 3770 (offset 1 line). Hunk #5 succeeded at 3780 (offset 1 line). patching file setup.py Hunk #1 succeeded at 200 (offset 40 lines). **************************************************** Host system: Darwin Zacharys-MBP.fios-router.home 18.7.0 Darwin Kernel Version 18.7.0: Sun Dec 1 18:59:03 PST 2019; root:xnu-4903.278.19~1/RELEASE_X86_64 x86_64 **************************************************** C compiler: gcc C compiler version: Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/c++/4.2.1 Apple LLVM version 10.0.1 (clang-1001.0.46.4) Target: x86_64-apple-darwin18.7.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin **************************************************** Uninstalling existing 'rpy2' Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__/__init__.cpython-37.pyc' not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__/test_dplyr.cpython-37.pyc' not found Warning: Directory '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__' not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__/test_ggplot2.cpython-37.pyc' not found Warning: Directory '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__' not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__/test_grdevices.cpython-37.pyc' not found Warning: Directory '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__' not 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not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/rlike/tests/__pycache__/__init__.cpython-37.pyc' not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/rlike/tests/__pycache__/test_container.cpython-37.pyc' not found Warning: Directory '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/rlike/tests/__pycache__' not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/rlike/tests/__pycache__/test_functional.cpython-37.pyc' not found Warning: Directory '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/rlike/tests/__pycache__' not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/rlike/tests/__pycache__/test_indexing.cpython-37.pyc' not found 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'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/__pycache__/language.cpython-37.pyc' not found Warning: Directory '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/__pycache__' not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/__pycache__/methods.cpython-37.pyc' not found Warning: Directory '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/__pycache__' not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/__pycache__/numpy2ri.cpython-37.pyc' not found Warning: Directory '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/__pycache__' not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/__pycache__/packages.cpython-37.pyc' not found Warning: Directory '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/__pycache__' not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/__pycache__/packages_utils.cpython-37.pyc' not found Warning: Directory '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/__pycache__' not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/__pycache__/pandas2ri.cpython-37.pyc' not found Warning: Directory '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/__pycache__' not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/__pycache__/robject.cpython-37.pyc' not found Warning: Directory '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/__pycache__' not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/__pycache__/vectors.cpython-37.pyc' not found Warning: Directory '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/__pycache__' not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/__pycache__/__init__.cpython-37.pyc' not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/__pycache__/rpy_classic.cpython-37.pyc' not found Warning: Directory '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/__pycache__' not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/__pycache__/tests.cpython-37.pyc' not found Warning: Directory '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/__pycache__' not found Warning: File '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/__pycache__/tests_rpy_classic.cpython-37.pyc' not found Warning: Directory '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/__pycache__' not found Removing stamp file '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/var/lib/sage/installed/rpy2-2.8.2.p1' Installing rpy2-2.8.2.p1 dyld: lazy symbol binding failed: Symbol not found: _timespec_get Referenced from: /Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/R/lib/libR.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: _timespec_get Referenced from: /Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/R/lib/libR.dylib Expected in: /usr/lib/libSystem.B.dylib Traceback (most recent call last): File "setup.py", line 331, in <module> ri_ext = getRinterface_ext() File "setup.py", line 234, in getRinterface_ext if rexec.version[0] == 'development' or \ File "setup.py", line 160, in version universal_newlines = True) File "/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/subprocess.py", line 395, in check_output **kwargs).stdout File "/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/subprocess.py", line 487, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '('/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/R/bin/R', '--version')' died with <Signals.SIGABRT: 6>. Error: could not determine package name ******************************************************************************** Error installing rpy2-2.8.2.p1 ******************************************************************************** real 0m0.480s user 0m0.296s sys 0m0.144s ************************************************************************ Error installing package rpy2-2.8.2.p1 ************************************************************************ Please email sage-devel (http://groups.google.com/group/sage-devel) explaining the problem and including the log file /Applications/SageMath-9.0.app/Contents/Resources/sage/logs/pkgs/rpy2-2.8.2.p1.log Describe your computer, operating system, etc. If you want to try to fix the problem yourself, *don't* just cd to /Applications/SageMath-9.0.app/Contents/Resources/sage/local/var/tmp/sage/build/rpy2-2.8.2.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 '/Applications/SageMath-9.0.app/Contents/Resources/sage/local/var/tmp/sage/build/rpy2-2.8.2.p1' && '/Applications/SageMath-9.0.app/Contents/Resources/sage/sage' --sh) When you are done debugging, you can type "exit" to leave the subshell. ************************************************************************
