Comments (10)
JBGreisman
commented on June 12, 2024
3
I can reproduce this issue on my mac, but I agree with @wojdyr's inclination that this may be a "wait and see" sort of issue. These are not the only packages that seem to be facing such an issue: numpy/numpy#17777
Based on that numpy issue, I tried the following:
export AR=/usr/bin/ar
Setting this environment variable does fix the issue for me and allows gemmi 0.4.3 to build successfully.
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JBGreisman
commented on June 12, 2024
1
I modified the title because it seems like the scope of this problem is restricted to macOS
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JBGreisman
commented on June 12, 2024
Thanks Minhuan -- I'll have a bit more of a look. I haven't yet added python 3.9 to the build matrix for our CI, so I should do that soon. Based on the error message, this seems to be on gemmi, but I'll look in a bit.
Just a note about install times -- it is notably faster on linux because gemmi has build wheels set up for linux. On MacOS it needs to build gemmi from source, which takes notably longer (minutes).
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wojdyr
commented on June 12, 2024
I can't reproduce it, so the error message would help (pip install -v gemmi).
You could also install binaries from conda-forge:
https://anaconda.org/conda-forge/gemmi/files?version=0.4.3
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kmdalton
commented on June 12, 2024
I was able to install under Python 3.9.1 on
Linux pop-os 5.8.0-7630-generic #32~1607010078~20.04~383a644-Ubuntu SMP Thu Dec 3 19:14:47 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
without issue. So, the Linux binaries seem to be good.
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minhuanli
commented on June 12, 2024
You are so responsive, I paste all the error message here. I am on macOS 10.15.7
Building wheel for gemmi (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /opt/miniconda3/envs/rs_test/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-x7ncgahi/gemmi_dd35e9a9407f41cab74cac04fb087c21/setup.py'"'"'; __file__='"'"'/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-x7ncgahi/gemmi_dd35e9a9407f41cab74cac04fb087c21/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-wheel-tar2v8o5
cwd: /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-x7ncgahi/gemmi_dd35e9a9407f41cab74cac04fb087c21/
Complete output (44 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.9
creating build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/hello.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/mtz_i_sigi.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/simple_search.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/aafreq.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/rama_gather.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/ccd_subgraph.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/matthews.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/rama_plot.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/__init__.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/mtrix_iso.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/maskdiff.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/sub_ccd.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/weight.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/from_json.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/cif_i_sigi.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/map2mtz.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/ccd_gi.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/patterson_slice.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/col_order.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/monomers.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/__main__.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/long_geom.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/merge_mtz_mmcif.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
running build_clib
building 'gemmi_zlib' library
creating build/temp.macosx-10.9-x86_64-3.9
creating build/temp.macosx-10.9-x86_64-3.9/third_party
creating build/temp.macosx-10.9-x86_64-3.9/third_party/zlib
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/adler32.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/adler32.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/crc32.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/crc32.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/gzlib.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzlib.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/gzread.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzread.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/inflate.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inflate.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/inftrees.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inftrees.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/inffast.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inffast.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/zutil.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/zutil.o
/opt/concourse/worker/volumes/live/ea4aade2-e62c-4ad6-5f84-14b9d4fda438/volume/python-split_1607696573928/_build_env/bin/llvm-ar rcs build/temp.macosx-10.9-x86_64-3.9/libgemmi_zlib.a build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/adler32.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/crc32.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzlib.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzread.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inflate.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inftrees.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inffast.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/zutil.o
error: command '/opt/concourse/worker/volumes/live/ea4aade2-e62c-4ad6-5f84-14b9d4fda438/volume/python-split_1607696573928/_build_env/bin/llvm-ar' failed: No such file or directory
----------------------------------------
ERROR: Failed building wheel for gemmi
Running setup.py clean for gemmi
Failed to build gemmi
Installing collected packages: wcwidth, six, ptyprocess, parso, ipython-genutils, traitlets, pytz, python-dateutil, pygments, pybind11, prompt-toolkit, pickleshare, pexpect, numpy, jedi, decorator, backcall, appnope, scipy, pandas, ipython, gemmi, reciprocalspaceship
Running setup.py install for gemmi ... error
ERROR: Command errored out with exit status 1:
command: /opt/miniconda3/envs/rs_test/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-x7ncgahi/gemmi_dd35e9a9407f41cab74cac04fb087c21/setup.py'"'"'; __file__='"'"'/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-x7ncgahi/gemmi_dd35e9a9407f41cab74cac04fb087c21/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-record-y2qb_dda/install-record.txt --single-version-externally-managed --compile --install-headers /opt/miniconda3/envs/rs_test/include/python3.9/gemmi
cwd: /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-x7ncgahi/gemmi_dd35e9a9407f41cab74cac04fb087c21/
Complete output (44 lines):
running install
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.9
creating build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/hello.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/mtz_i_sigi.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/simple_search.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/aafreq.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/rama_gather.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/ccd_subgraph.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/matthews.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/rama_plot.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/__init__.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/mtrix_iso.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/maskdiff.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/sub_ccd.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/weight.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/from_json.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/cif_i_sigi.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/map2mtz.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/ccd_gi.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/patterson_slice.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/col_order.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/monomers.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/__main__.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/long_geom.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/merge_mtz_mmcif.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
running build_clib
building 'gemmi_zlib' library
creating build/temp.macosx-10.9-x86_64-3.9
creating build/temp.macosx-10.9-x86_64-3.9/third_party
creating build/temp.macosx-10.9-x86_64-3.9/third_party/zlib
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/adler32.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/adler32.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/crc32.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/crc32.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/gzlib.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzlib.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/gzread.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzread.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/inflate.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inflate.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/inftrees.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inftrees.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/inffast.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inffast.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/zutil.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/zutil.o
/opt/concourse/worker/volumes/live/ea4aade2-e62c-4ad6-5f84-14b9d4fda438/volume/python-split_1607696573928/_build_env/bin/llvm-ar rcs build/temp.macosx-10.9-x86_64-3.9/libgemmi_zlib.a build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/adler32.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/crc32.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzlib.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzread.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inflate.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inftrees.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inffast.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/zutil.o
error: command '/opt/concourse/worker/volumes/live/ea4aade2-e62c-4ad6-5f84-14b9d4fda438/volume/python-split_1607696573928/_build_env/bin/llvm-ar' failed: No such file or directory
----------------------------------------
ERROR: Command errored out with exit status 1: /opt/miniconda3/envs/rs_test/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-x7ncgahi/gemmi_dd35e9a9407f41cab74cac04fb087c21/setup.py'"'"'; __file__='"'"'/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-x7ncgahi/gemmi_dd35e9a9407f41cab74cac04fb087c21/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-record-y2qb_dda/install-record.txt --single-version-externally-managed --compile --install-headers /opt/miniconda3/envs/rs_test/include/python3.9/gemmi Check the logs for full command output.
from reciprocalspaceship.
minhuanli
commented on June 12, 2024
And here is the error message after pip install -v gemmi:
Using pip 20.3.3 from /opt/miniconda3/envs/rs_test/lib/python3.9/site-packages/pip (python 3.9)
Non-user install because site-packages writeable
Created temporary directory: /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-ephem-wheel-cache-kaxuazok
Created temporary directory: /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-req-tracker-v01z3vza
Initialized build tracking at /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-req-tracker-v01z3vza
Created build tracker: /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-req-tracker-v01z3vza
Entered build tracker: /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-req-tracker-v01z3vza
Created temporary directory: /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-8qma2c_z
1 location(s) to search for versions of gemmi:
* https://pypi.org/simple/gemmi/
Fetching project page and analyzing links: https://pypi.org/simple/gemmi/
Getting page https://pypi.org/simple/gemmi/
Found index url https://pypi.org/simple
Looking up "https://pypi.org/simple/gemmi/" in the cache
Request header has "max_age" as 0, cache bypassed
Starting new HTTPS connection (1): pypi.org:443
https://pypi.org:443 "GET /simple/gemmi/ HTTP/1.1" 304 0
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Skipping link: none of the wheel's tags match: cp38-cp38-win32: https://files.pythonhosted.org/packages/ad/37/dd827724ae053469469c4dc3f050b5b16093195fa50030a202a593fb380a/gemmi-0.4.3-cp38-cp38-win32.whl#sha256=9b13da898e62666249251a358f10087ffdac2bcf8734bb1780b54fda263babc8 (from https://pypi.org/simple/gemmi/)
Skipping link: none of the wheel's tags match: cp38-cp38-win_amd64: https://files.pythonhosted.org/packages/cd/15/4460162edf9aea5c568b6fbdf2b55536800b32e639064db8fb112c779edf/gemmi-0.4.3-cp38-cp38-win_amd64.whl#sha256=e70501c35e56ec6dafd8a2d64d74a3e5cf32fc87c5934d5ca68ad077bb0fe042 (from https://pypi.org/simple/gemmi/)
Skipping link: none of the wheel's tags match: cp39-cp39-manylinux2010_x86_64: https://files.pythonhosted.org/packages/4d/35/e8b97d567e27090876330931af7a5f097aed5387067718a25a9d4225ff82/gemmi-0.4.3-cp39-cp39-manylinux2010_x86_64.whl#sha256=f2b50d47148bb02c0cade07d936c27efd56aa192b871cbd05c50e815f0f5189c (from https://pypi.org/simple/gemmi/)
Found link https://files.pythonhosted.org/packages/b7/6b/b4c5c2c12da58813f2478fdffac17d86aaf46c570b6f8b42eef9778d8180/gemmi-0.4.3.tar.gz#sha256=dd1f9d3b5ae06593f15e3093db5a41e6d4609307888ed3b25388087eae7ad9d3 (from https://pypi.org/simple/gemmi/), version: 0.4.3
Given no hashes to check 26 links for project 'gemmi': discarding no candidates
Collecting gemmi
Created temporary directory: /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-unpack-x6rzzogn
Looking up "https://files.pythonhosted.org/packages/b7/6b/b4c5c2c12da58813f2478fdffac17d86aaf46c570b6f8b42eef9778d8180/gemmi-0.4.3.tar.gz" in the cache
Current age based on date: 272950
Ignoring unknown cache-control directive: immutable
Freshness lifetime from max-age: 365000000
The response is "fresh", returning cached response
365000000 > 272950
Using cached gemmi-0.4.3.tar.gz (578 kB)
Added gemmi from https://files.pythonhosted.org/packages/b7/6b/b4c5c2c12da58813f2478fdffac17d86aaf46c570b6f8b42eef9778d8180/gemmi-0.4.3.tar.gz#sha256=dd1f9d3b5ae06593f15e3093db5a41e6d4609307888ed3b25388087eae7ad9d3 to build tracker '/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-req-tracker-v01z3vza'
Running setup.py (path:/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-8qma2c_z/gemmi_26015705375f4eb1aab865cfc994bbe5/setup.py) egg_info for package gemmi
Created temporary directory: /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-pip-egg-info-x1d2xw4f
Running command python setup.py egg_info
running egg_info
creating /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-pip-egg-info-x1d2xw4f/gemmi.egg-info
writing /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-pip-egg-info-x1d2xw4f/gemmi.egg-info/PKG-INFO
writing dependency_links to /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-pip-egg-info-x1d2xw4f/gemmi.egg-info/dependency_links.txt
writing requirements to /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-pip-egg-info-x1d2xw4f/gemmi.egg-info/requires.txt
writing top-level names to /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-pip-egg-info-x1d2xw4f/gemmi.egg-info/top_level.txt
writing manifest file '/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-pip-egg-info-x1d2xw4f/gemmi.egg-info/SOURCES.txt'
reading manifest file '/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-pip-egg-info-x1d2xw4f/gemmi.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file '/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-pip-egg-info-x1d2xw4f/gemmi.egg-info/SOURCES.txt'
Source in /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-8qma2c_z/gemmi_26015705375f4eb1aab865cfc994bbe5 has version 0.4.3, which satisfies requirement gemmi from https://files.pythonhosted.org/packages/b7/6b/b4c5c2c12da58813f2478fdffac17d86aaf46c570b6f8b42eef9778d8180/gemmi-0.4.3.tar.gz#sha256=dd1f9d3b5ae06593f15e3093db5a41e6d4609307888ed3b25388087eae7ad9d3
Removed gemmi from https://files.pythonhosted.org/packages/b7/6b/b4c5c2c12da58813f2478fdffac17d86aaf46c570b6f8b42eef9778d8180/gemmi-0.4.3.tar.gz#sha256=dd1f9d3b5ae06593f15e3093db5a41e6d4609307888ed3b25388087eae7ad9d3 from build tracker '/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-req-tracker-v01z3vza'
1 location(s) to search for versions of pybind11:
* https://pypi.org/simple/pybind11/
Fetching project page and analyzing links: https://pypi.org/simple/pybind11/
Getting page https://pypi.org/simple/pybind11/
Found index url https://pypi.org/simple
Looking up "https://pypi.org/simple/pybind11/" in the cache
Request header has "max_age" as 0, cache bypassed
https://pypi.org:443 "GET /simple/pybind11/ HTTP/1.1" 304 0
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Found link https://files.pythonhosted.org/packages/6d/ac/5feda51a305a74ce4f8d6de09de3d8b40e58e72750181fc389b9ff45d215/pybind11-2.6.0b1.tar.gz#sha256=620d7b6f60d7d8fa1f3ea869484950eeae439dae1d3fff118e93cc05e0a52fae (from https://pypi.org/simple/pybind11/) (requires-python:!=3.0,!=3.1,!=3.2,!=3.3,!=3.4,>=2.7), version: 2.6.0b1
Found link https://files.pythonhosted.org/packages/56/df/e4e5da73e024c57fa6d355f2d8daed40641ac1b8c83cb2785874e591efa1/pybind11-2.6.0rc1-py2.py3-none-any.whl#sha256=471c5dec187659fc93de80c52198b00750aaa9f6f9121871c9aff36426910227 (from https://pypi.org/simple/pybind11/) (requires-python:!=3.0,!=3.1,!=3.2,!=3.3,!=3.4,>=2.7), version: 2.6.0rc1
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Found link https://files.pythonhosted.org/packages/7f/75/4e76b04fe24ca5fba19ee1691305232c080395cf49ae55fb5f2e32b95416/pybind11-2.6.0rc2-py2.py3-none-any.whl#sha256=c8be6893b88b4c23acf09e3789a2d883abf2475658ba3880b8b3600ad49e215b (from https://pypi.org/simple/pybind11/) (requires-python:!=3.0,!=3.1,!=3.2,!=3.3,!=3.4,>=2.7), version: 2.6.0rc2
Found link https://files.pythonhosted.org/packages/7a/32/a698ba4f25d5ab0eb450f8c387949315f0ad91eba555d7f37079639291ae/pybind11-2.6.0rc2.tar.gz#sha256=f9ba20fee8660f906b190dc45cb15acc47ae42576d1a2b5b354447cf8314c4ba (from https://pypi.org/simple/pybind11/) (requires-python:!=3.0,!=3.1,!=3.2,!=3.3,!=3.4,>=2.7), version: 2.6.0rc2
Found link https://files.pythonhosted.org/packages/fb/55/15c31b01a7905911e10b085394e9d40a2c2707a47e148ba099e9b7077a31/pybind11-2.6.0rc3-py2.py3-none-any.whl#sha256=a476244dc96920320df0149ddabec827fee93bbd44dd2953225a0b63f74a4c3c (from https://pypi.org/simple/pybind11/) (requires-python:!=3.0,!=3.1,!=3.2,!=3.3,!=3.4,>=2.7), version: 2.6.0rc3
Found link https://files.pythonhosted.org/packages/ec/96/bc203a96726a6c7bdf53e0c3bbf1a2f64c14d2c901c73eecebfe4961e814/pybind11-2.6.0rc3.tar.gz#sha256=5473b68eac2bf4e488fffb4120324e927faf3777556d9752b94f5b6667af5aa4 (from https://pypi.org/simple/pybind11/) (requires-python:!=3.0,!=3.1,!=3.2,!=3.3,!=3.4,>=2.7), version: 2.6.0rc3
Found link https://files.pythonhosted.org/packages/92/a5/796ccb611a92cbdf1f6eaa9b2ec9458d5784a7b909efdf8e8afaa3861783/pybind11-2.6.0-py2.py3-none-any.whl#sha256=4ddeee54adf844ce44801c32a61e1863dd79283a5ce7afbb96e05fe61fa1fd7d (from https://pypi.org/simple/pybind11/) (requires-python:!=3.0,!=3.1,!=3.2,!=3.3,!=3.4,>=2.7), version: 2.6.0
Found link https://files.pythonhosted.org/packages/9a/36/3a9de7b56e0b01689d9ca4658701d12941069940f8a1431597a48dbc53fa/pybind11-2.6.0.tar.gz#sha256=4107de1fd612bf52953fd64dab7f94f11d2ab3548e1b761cbf8ebc87a2480912 (from https://pypi.org/simple/pybind11/) (requires-python:!=3.0,!=3.1,!=3.2,!=3.3,!=3.4,>=2.7), version: 2.6.0
Found link https://files.pythonhosted.org/packages/00/84/fc9dc13ee536ba5e6b8fd10ce368fea5b738fe394c3b296cde7c9b144a92/pybind11-2.6.1-py2.py3-none-any.whl#sha256=c3691da74b670a4850dec30c1145a0dad53a50eeca78b7e7cdc855b5c98fd32d (from https://pypi.org/simple/pybind11/) (requires-python:!=3.0,!=3.1,!=3.2,!=3.3,!=3.4,>=2.7), version: 2.6.1
Found link https://files.pythonhosted.org/packages/d8/47/2eb4be23fa8cc1a08c855c012c1aa4348d06ab1a5527f876515bbf689644/pybind11-2.6.1.tar.gz#sha256=ab7e60a520fe6ae25eca939191bb2ac416cd58478ce754740238a8bf1af18934 (from https://pypi.org/simple/pybind11/) (requires-python:!=3.0,!=3.1,!=3.2,!=3.3,!=3.4,>=2.7), version: 2.6.1
Given no hashes to check 4 links for project 'pybind11': discarding no candidates
Collecting pybind11>=2.6.0
Created temporary directory: /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-unpack-yvj4_r1i
Looking up "https://files.pythonhosted.org/packages/00/84/fc9dc13ee536ba5e6b8fd10ce368fea5b738fe394c3b296cde7c9b144a92/pybind11-2.6.1-py2.py3-none-any.whl" in the cache
Current age based on date: 272950
Ignoring unknown cache-control directive: immutable
Freshness lifetime from max-age: 365000000
The response is "fresh", returning cached response
365000000 > 272950
Using cached pybind11-2.6.1-py2.py3-none-any.whl (188 kB)
Added pybind11>=2.6.0 from https://files.pythonhosted.org/packages/00/84/fc9dc13ee536ba5e6b8fd10ce368fea5b738fe394c3b296cde7c9b144a92/pybind11-2.6.1-py2.py3-none-any.whl#sha256=c3691da74b670a4850dec30c1145a0dad53a50eeca78b7e7cdc855b5c98fd32d (from gemmi) to build tracker '/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-req-tracker-v01z3vza'
Removed pybind11>=2.6.0 from https://files.pythonhosted.org/packages/00/84/fc9dc13ee536ba5e6b8fd10ce368fea5b738fe394c3b296cde7c9b144a92/pybind11-2.6.1-py2.py3-none-any.whl#sha256=c3691da74b670a4850dec30c1145a0dad53a50eeca78b7e7cdc855b5c98fd32d (from gemmi) from build tracker '/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-req-tracker-v01z3vza'
Created temporary directory: /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-unpack-sn650j8q
Building wheels for collected packages: gemmi
Created temporary directory: /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-wheel-sbc30nvu
Building wheel for gemmi (setup.py) ... Destination directory: /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-wheel-sbc30nvu
Running command /opt/miniconda3/envs/rs_test/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-8qma2c_z/gemmi_26015705375f4eb1aab865cfc994bbe5/setup.py'"'"'; __file__='"'"'/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-8qma2c_z/gemmi_26015705375f4eb1aab865cfc994bbe5/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-wheel-sbc30nvu
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.9
creating build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/hello.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/mtz_i_sigi.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/simple_search.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/aafreq.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/rama_gather.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/ccd_subgraph.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/matthews.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/rama_plot.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/__init__.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/mtrix_iso.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/maskdiff.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/sub_ccd.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/weight.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/from_json.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/cif_i_sigi.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/map2mtz.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/ccd_gi.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/patterson_slice.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/col_order.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/monomers.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/__main__.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/long_geom.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/merge_mtz_mmcif.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
running build_clib
building 'gemmi_zlib' library
creating build/temp.macosx-10.9-x86_64-3.9
creating build/temp.macosx-10.9-x86_64-3.9/third_party
creating build/temp.macosx-10.9-x86_64-3.9/third_party/zlib
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/adler32.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/adler32.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/crc32.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/crc32.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/gzlib.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzlib.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/gzread.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzread.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/inflate.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inflate.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/inftrees.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inftrees.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/inffast.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inffast.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/zutil.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/zutil.o
/opt/concourse/worker/volumes/live/ea4aade2-e62c-4ad6-5f84-14b9d4fda438/volume/python-split_1607696573928/_build_env/bin/llvm-ar rcs build/temp.macosx-10.9-x86_64-3.9/libgemmi_zlib.a build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/adler32.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/crc32.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzlib.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzread.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inflate.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inftrees.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inffast.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/zutil.o
error: command '/opt/concourse/worker/volumes/live/ea4aade2-e62c-4ad6-5f84-14b9d4fda438/volume/python-split_1607696573928/_build_env/bin/llvm-ar' failed: No such file or directory
error
ERROR: Failed building wheel for gemmi
Running setup.py clean for gemmi
Running command /opt/miniconda3/envs/rs_test/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-8qma2c_z/gemmi_26015705375f4eb1aab865cfc994bbe5/setup.py'"'"'; __file__='"'"'/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-8qma2c_z/gemmi_26015705375f4eb1aab865cfc994bbe5/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
running clean
removing 'build/temp.macosx-10.9-x86_64-3.9' (and everything under it)
removing 'build/lib.macosx-10.9-x86_64-3.9' (and everything under it)
'build/bdist.macosx-10.9-x86_64' does not exist -- can't clean it
'build/scripts-3.9' does not exist -- can't clean it
removing 'build'
Failed to build gemmi
Installing collected packages: pybind11, gemmi
changing mode of /opt/miniconda3/envs/rs_test/bin/pybind11-config to 755
Created temporary directory: /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-record-gn_tpk_6
Running command /opt/miniconda3/envs/rs_test/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-8qma2c_z/gemmi_26015705375f4eb1aab865cfc994bbe5/setup.py'"'"'; __file__='"'"'/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-8qma2c_z/gemmi_26015705375f4eb1aab865cfc994bbe5/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-record-gn_tpk_6/install-record.txt --single-version-externally-managed --compile --install-headers /opt/miniconda3/envs/rs_test/include/python3.9/gemmi
running install
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.9
creating build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/hello.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/mtz_i_sigi.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/simple_search.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/aafreq.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/rama_gather.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/ccd_subgraph.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/matthews.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/rama_plot.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/__init__.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/mtrix_iso.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/maskdiff.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/sub_ccd.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/weight.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/from_json.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/cif_i_sigi.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/map2mtz.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/ccd_gi.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/patterson_slice.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/col_order.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/monomers.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/__main__.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/long_geom.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
copying examples/merge_mtz_mmcif.py -> build/lib.macosx-10.9-x86_64-3.9/gemmi-examples
running build_clib
building 'gemmi_zlib' library
creating build/temp.macosx-10.9-x86_64-3.9
creating build/temp.macosx-10.9-x86_64-3.9/third_party
creating build/temp.macosx-10.9-x86_64-3.9/third_party/zlib
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/adler32.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/adler32.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/crc32.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/crc32.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/gzlib.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzlib.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/gzread.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzread.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/inflate.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inflate.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/inftrees.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inftrees.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/inffast.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inffast.o
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -fPIC -O2 -isystem /opt/miniconda3/envs/rs_test/include -arch x86_64 -DNO_GZCOMPRESS=1 -DZ_HAVE_UNISTD_H=1 -c third_party/zlib/zutil.c -o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/zutil.o
/opt/concourse/worker/volumes/live/ea4aade2-e62c-4ad6-5f84-14b9d4fda438/volume/python-split_1607696573928/_build_env/bin/llvm-ar rcs build/temp.macosx-10.9-x86_64-3.9/libgemmi_zlib.a build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/adler32.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/crc32.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzlib.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzread.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inflate.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inftrees.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inffast.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/zutil.o
error: command '/opt/concourse/worker/volumes/live/ea4aade2-e62c-4ad6-5f84-14b9d4fda438/volume/python-split_1607696573928/_build_env/bin/llvm-ar' failed: No such file or directory
Running setup.py install for gemmi ... error
ERROR: Command errored out with exit status 1: /opt/miniconda3/envs/rs_test/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-8qma2c_z/gemmi_26015705375f4eb1aab865cfc994bbe5/setup.py'"'"'; __file__='"'"'/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-8qma2c_z/gemmi_26015705375f4eb1aab865cfc994bbe5/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-record-gn_tpk_6/install-record.txt --single-version-externally-managed --compile --install-headers /opt/miniconda3/envs/rs_test/include/python3.9/gemmi Check the logs for full command output.
Exception information:
Traceback (most recent call last):
File "/opt/miniconda3/envs/rs_test/lib/python3.9/site-packages/pip/_internal/req/req_install.py", line 840, in install
success = install_legacy(
File "/opt/miniconda3/envs/rs_test/lib/python3.9/site-packages/pip/_internal/operations/install/legacy.py", line 86, in install
raise LegacyInstallFailure
pip._internal.operations.install.legacy.LegacyInstallFailure
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda3/envs/rs_test/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 224, in _main
status = self.run(options, args)
File "/opt/miniconda3/envs/rs_test/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 180, in wrapper
return func(self, options, args)
File "/opt/miniconda3/envs/rs_test/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 394, in run
installed = install_given_reqs(
File "/opt/miniconda3/envs/rs_test/lib/python3.9/site-packages/pip/_internal/req/__init__.py", line 82, in install_given_reqs
requirement.install(
File "/opt/miniconda3/envs/rs_test/lib/python3.9/site-packages/pip/_internal/req/req_install.py", line 858, in install
six.reraise(*exc.parent)
File "/opt/miniconda3/envs/rs_test/lib/python3.9/site-packages/pip/_vendor/six.py", line 703, in reraise
raise value
File "/opt/miniconda3/envs/rs_test/lib/python3.9/site-packages/pip/_internal/operations/install/legacy.py", line 74, in install
runner(
File "/opt/miniconda3/envs/rs_test/lib/python3.9/site-packages/pip/_internal/utils/subprocess.py", line 271, in runner
call_subprocess(
File "/opt/miniconda3/envs/rs_test/lib/python3.9/site-packages/pip/_internal/utils/subprocess.py", line 240, in call_subprocess
raise InstallationError(exc_msg)
pip._internal.exceptions.InstallationError: Command errored out with exit status 1: /opt/miniconda3/envs/rs_test/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-8qma2c_z/gemmi_26015705375f4eb1aab865cfc994bbe5/setup.py'"'"'; __file__='"'"'/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-install-8qma2c_z/gemmi_26015705375f4eb1aab865cfc994bbe5/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-record-gn_tpk_6/install-record.txt --single-version-externally-managed --compile --install-headers /opt/miniconda3/envs/rs_test/include/python3.9/gemmi Check the logs for full command output.
Removed build tracker: '/private/var/folders/9k/1fwhk9v17bv7t49qyr_6zgg40000gn/T/pip-req-tracker-v01z3vza'
from reciprocalspaceship.
minhuanli
commented on June 12, 2024
I can't reproduce it, so the error message would help (pip install -v gemmi).
You could also install binaries from conda-forge:
https://anaconda.org/conda-forge/gemmi/files?version=0.4.3
conda install -c conda-forge gemmi works well in this 3.9 env.
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wojdyr
commented on June 12, 2024
The error seems to be that setuptools(?) expect llvm-ar in the build environent:
/opt/concourse/worker/volumes/live/ea4aade2-e62c-4ad6-5f84-14b9d4fda438/volume/python-split_1607696573928/_build_env/bin/llvm-ar rcs build/temp.macosx-10.9-x86_64-3.9/libgemmi_zlib.a build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/adler32.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/crc32.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzlib.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/gzread.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inflate.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inftrees.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/inffast.o build/temp.macosx-10.9-x86_64-3.9/third_party/zlib/zutil.o
error: command '/opt/concourse/worker/volumes/live/ea4aade2-e62c-4ad6-5f84-14b9d4fda438/volume/python-split_1607696573928/_build_env/bin/llvm-ar' failed: No such file or directory
I don't know what is the cause. I'll pass on it, hoping that this error will vanish at some point.
from reciprocalspaceship.
JBGreisman
commented on June 12, 2024
I'm going to close this issue because @wojdyr has now set up gemmi wheel releases for macOS (including python3.9): project-gemmi/gemmi#42.
I can now pip install reciprocalspaceship into a python3.9 environment on macOS without build issues (and without needing the above environment variable)
@minhuanli please feel free to re-open if you run into any more issues
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Related Issues (20)
- Add `sample_rate` or `resolution_cutoff` options for `to_reciprocalgrid` HOT 5
- rs.DataSet.assign_resolution_bins ought to return bin edges HOT 1
- Cannot unstack_anomalous with other columns in index
- groupby apply drops cell and spacegroup HOT 2
- `stack_anomalous` inside `groupby` breaks `as_index=False` HOT 1
- Unstack anomalous taking into account Careless repeats HOT 10
- rs.utils.asu.in_asu() does not use the 'anomalous ASU' for stacked anomalous data. HOT 1
- function for cif file IO and possible support for multi-dataset files HOT 3
- `hkl_to_asu` does not annotate M/ISYM field correctly HOT 2
- support for read_precognition() for hkl without anomalous columns HOT 6
- unstack_anomalous makes data that phenix cannot interpret HOT 3
- API reference website display
- Return keys of dictionary in crystfel.py HOT 6
- add_rfree() does not consider Friedel mates HOT 2
- `rs.DataSet.reset_index()` call signature does not match pandas >1.5 HOT 1
- Used pandas.core.ops attribute does not appear to exist HOT 4
- A `rs.cifdump` utility? HOT 1
- No documentation of CrystFEL columns HOT 1
- mean_intensity_by_miller_index should use a grid HOT 1
- write_mtz SettingWithCopyWarning HOT 2
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