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jmol init, pymol -> 2.1.0 and tidied up all-packages.nix #37855

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merged 3 commits into from May 1, 2018
Merged

jmol init, pymol -> 2.1.0 and tidied up all-packages.nix #37855

merged 3 commits into from May 1, 2018

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Mounium
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@Mounium Mounium commented Mar 26, 2018

Motivation for this change
Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option build-use-sandbox in nix.conf on non-NixOS)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Fits CONTRIBUTING.md.

@Mounium Mounium changed the title Chemistry-related commits, jmol init, pymol -> 2.1.0 and tidied up all-packages.nix jmol init, pymol -> 2.1.0 and tidied up all-packages.nix Mar 26, 2018
matthewbauer
matthewbauer requested changes Apr 25, 2018
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Resolve merge conflicts.

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Mounium commented Apr 25, 2018

@matthewbauer

bin/jmol: line 20: /bin/ls: No such file or directory
bin/jmol: line 21: /usr/bin/expr: No such file or directory
bin/jmol: line 22: /usr/bin/expr: No such file or directory
bin/jmol: line 25: /usr/bin/dirname: No such file or directory

I got this error while executing the jmol symlink, solved by using patched original initiation script.

I also rebased branch, so there won't be two jmol lines in all-packages.nix

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@GrahamcOfBorg build jmol pymol

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Success on aarch64-linux (full log)

Attempted: pymol

The following builds were skipped because they don't evaluate on aarch64-linux: jmol

Partial log (click to expand)

writing manifest file 'pymol.egg-info/SOURCES.txt'
running build_ext
copying build/lib.linux-aarch64-3.6/pymol/_cmd.cpython-36m-aarch64-linux-gnu.so -> modules/pymol
copying build/lib.linux-aarch64-3.6/chempy/champ/_champ.cpython-36m-aarch64-linux-gnu.so -> modules/chempy/champ

----------------------------------------------------------------------
Ran 0 tests in 0.000s

OK
/nix/store/a3zsgv9h3qj6mj4pxpa90dcszyjkqr3v-pymol-2.1.0

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Failure on x86_64-darwin (full log)

Attempted: jmol, pymol

Partial log (click to expand)

clang++ -std=c++0x -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_FREETYPE -DNO_MMLIBS -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/nix/store/8jcsbs0m9hklh01mmh2ydnhw1mrgsy6i-python3.6-numpy-1.14.2/lib/python3.6/site-packages/numpy/core/include -I/nix/store/sm6n6vgc3gy064nnvc49b5g8a6n2cn8h-python3-3.6.5/include/python3.6m -c modules/cealign/src/ccealignmodule.cpp -o build/temp.macosx-10.6-x86_64-3.6/modules/cealign/src/ccealignmodule.o -Wno-write-strings -Wno-unused-function -Wno-char-subscripts -ffast-math -funroll-loops -fcommon
clang++ -std=c++0x -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_FREETYPE -DNO_MMLIBS -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/nix/store/8jcsbs0m9hklh01mmh2ydnhw1mrgsy6i-python3.6-numpy-1.14.2/lib/python3.6/site-packages/numpy/core/include -I/nix/store/sm6n6vgc3gy064nnvc49b5g8a6n2cn8h-python3-3.6.5/include/python3.6m -c layer3/Selector.cpp -o build/temp.macosx-10.6-x86_64-3.6/layer3/Selector.o -Wno-write-strings -Wno-unused-function -Wno-char-subscripts -ffast-math -funroll-loops -fcommon
clang++ -std=c++0x -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_FREETYPE -DNO_MMLIBS -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/nix/store/8jcsbs0m9hklh01mmh2ydnhw1mrgsy6i-python3.6-numpy-1.14.2/lib/python3.6/site-packages/numpy/core/include -I/nix/store/sm6n6vgc3gy064nnvc49b5g8a6n2cn8h-python3-3.6.5/include/python3.6m -c ov/src/OVContext.cpp -o build/temp.macosx-10.6-x86_64-3.6/ov/src/OVContext.o -Wno-write-strings -Wno-unused-function -Wno-char-subscripts -ffast-math -funroll-loops -fcommon
clang++ -std=c++0x -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_FREETYPE -DNO_MMLIBS -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/nix/store/8jcsbs0m9hklh01mmh2ydnhw1mrgsy6i-python3.6-numpy-1.14.2/lib/python3.6/site-packages/numpy/core/include -I/nix/store/sm6n6vgc3gy064nnvc49b5g8a6n2cn8h-python3-3.6.5/include/python3.6m -c layer4/Cmd.cpp -o build/temp.macosx-10.6-x86_64-3.6/layer4/Cmd.o -Wno-write-strings -Wno-unused-function -Wno-char-subscripts -ffast-math -funroll-loops -fcommon
clang++ -std=c++0x -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_FREETYPE -DNO_MMLIBS -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/nix/store/8jcsbs0m9hklh01mmh2ydnhw1mrgsy6i-python3.6-numpy-1.14.2/lib/python3.6/site-packages/numpy/core/include -I/nix/store/sm6n6vgc3gy064nnvc49b5g8a6n2cn8h-python3-3.6.5/include/python3.6m -c layer4/Export.cpp -o build/temp.macosx-10.6-x86_64-3.6/layer4/Export.o -Wno-write-strings -Wno-unused-function -Wno-char-subscripts -ffast-math -funroll-loops -fcommon
clang++ -std=c++0x -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_FREETYPE -DNO_MMLIBS -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/nix/store/8jcsbs0m9hklh01mmh2ydnhw1mrgsy6i-python3.6-numpy-1.14.2/lib/python3.6/site-packages/numpy/core/include -I/nix/store/sm6n6vgc3gy064nnvc49b5g8a6n2cn8h-python3-3.6.5/include/python3.6m -c layer1/Shaker.cpp -o build/temp.macosx-10.6-x86_64-3.6/layer1/Shaker.o -Wno-write-strings -Wno-unused-function -Wno-char-subscripts -ffast-math -funroll-loops -fcommon
clang++ -std=c++0x -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_FREETYPE -DNO_MMLIBS -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/nix/store/8jcsbs0m9hklh01mmh2ydnhw1mrgsy6i-python3.6-numpy-1.14.2/lib/python3.6/site-packages/numpy/core/include -I/nix/store/sm6n6vgc3gy064nnvc49b5g8a6n2cn8h-python3-3.6.5/include/python3.6m -c layer1/Symmetry.cpp -o build/temp.macosx-10.6-x86_64-3.6/layer1/Symmetry.o -Wno-write-strings -Wno-unused-function -Wno-char-subscripts -ffast-math -funroll-loops -fcommon
error: command 'clang++' failed with exit status 70
builder for '/nix/store/mjwaba6iyqa0xwa68jcsfi9arwrfln5f-pymol-2.1.0.drv' failed with exit code 1
�[31;1merror:�[0m build of '/nix/store/mjwaba6iyqa0xwa68jcsfi9arwrfln5f-pymol-2.1.0.drv' failed

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Success on x86_64-linux (full log)

Attempted: jmol, pymol

Partial log (click to expand)

reading manifest file 'pymol.egg-info/SOURCES.txt'
writing manifest file 'pymol.egg-info/SOURCES.txt'
running build_ext
copying build/lib.linux-x86_64-3.6/pymol/_cmd.cpython-36m-x86_64-linux-gnu.so -> modules/pymol
copying build/lib.linux-x86_64-3.6/chempy/champ/_champ.cpython-36m-x86_64-linux-gnu.so -> modules/chempy/champ

----------------------------------------------------------------------
Ran 0 tests in 0.000s

OK

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Mounium commented May 1, 2018

@matthewbauer Could you please merge it if you think it is useful, because I'm afraid the change to all-packages.nix will sooner or later will conflict with the base branch.

Also, I don't know should anything be done about darwin or is it ok to let it fail?

@matthewbauer matthewbauer merged commit 63666bf into NixOS:master May 1, 2018
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