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mxnet: 1.1.0 -> 1.2.0 #42807

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wants to merge 4 commits into from
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mxnet: 1.1.0 -> 1.2.0 #42807

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grwlf
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@grwlf grwlf commented Jun 30, 2018

Motivation for this change

The following patches update mxnet to version 1.2.0 and move it from math to machine-learning folder

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option 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/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Fits CONTRIBUTING.md.

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Please split the first commit into 2 separate ones.

@@ -10119,11 +10119,11 @@ in {

graphviz = buildPythonPackage rec {
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This package needs to be moved out of python-packages.nix.

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(deleted question about the location. going to add under development/python-modules)

@@ -10119,11 +10119,11 @@ in {

graphviz = buildPythonPackage rec {
name = "graphviz-${version}";
version = "0.5.2";
version = "0.8.1";

src = pkgs.fetchurl {
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fetchPypi

@@ -10119,11 +10119,11 @@ in {

graphviz = buildPythonPackage rec {
name = "graphviz-${version}";
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Please specify pname instead.

@@ -2800,6 +2800,8 @@ in {

mpyq = callPackage ../development/python-modules/mpyq { };

onnx = callPackage ../development/python-modules/onnx { };
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The attributes should be ordered alphabetically.

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FIxed

@@ -14585,6 +14587,17 @@ in {

typing = callPackage ../development/python-modules/typing { };

typing-extensions = buildPythonPackage rec {
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This is already packaged as typing-extensions I believe.

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Do you mean there is a conflict with some newer version of nixpkgs?

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This package simply already exists. However, that's on the master branch only. Anyway, you should make your pull request against master as explained in https://nixos.org/nixpkgs/manual/#chap-submitting-changes

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Manual says "You can make branch from a commit of your local nixos-version. That will help you to avoid additional local compilations". I use separate nixpkgs tree for this PR and branched from nixos-18.03 of nixpkgs-channels. Is it wrong?

Should I cherry-pick typing-extensions commit from master to this PR in order for git-merge to handle it?

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I cite:

Rebase you branch against current master.

Someone should fix that typo though :D

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OK, found this place. Given the cite I made earlier, I should say the manual is somewhat misleading here.


propagatedBuildInputs = [ protobuf ];

buildInputs = [ cmake numpy mypy typing-extensions ] ;
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Why is mypy needed? numpy and typing-extensions probably belong into propagatedBuildInputs and cmake into nativeBuildInputs.

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@grwlf grwlf Jul 2, 2018

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Correct, mypy is probably a compile-time dep. Not sure about typing-extensions, but let it be propagated. Unfortunately, something is missing to produce types, but it is not critical. I put a fixme about that in the updated version of expression.

Edit: the warning text is Failed to generate mypy stubs: No module named 'google.protobuf.compiler'

};

# FIXME: Workaround 'ERROR: file not found: onnx/examples'. Maybe one shold
# try `fetchgit` instead of `fetchPypi`.
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Should I react to this?

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No, just wanted to let you know.

@grwlf grwlf force-pushed the mxnet branch 4 times, most recently from 43716bd to 57df1fe Compare July 7, 2018 10:08
@grwlf grwlf changed the base branch from release-18.03 to master July 7, 2018 10:11
# NOTE: We weaken requests requirenments to avoid backporting to
# requests-2.18. Newer version should not cause problems, according the
# changelog. See https://github.com/requests/requests/blob/master/HISTORY.rst
postPatch = ''
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You should probably use

sed -i 's/requests<2.19.0,>=2.18.4/requests<=2.20.0,>=2.18.4/g' setup.py

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<2.20.0. Done

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@GrahamcOfBorg build python2.pkgs.mxnet python3.pkgs.mxnet

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No attempt on x86_64-darwin (full log)

The following builds were skipped because they don't evaluate on x86_64-darwin: python2.pkgs.mxnet, python3.pkgs.mxnet

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnsupportedSystem = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnsupportedSystem = true; }
to ~/.config/nixpkgs/config.nix.


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Failure on aarch64-linux (full log)

Attempted: python2.pkgs.mxnet, python3.pkgs.mxnet

Partial log (click to expand)

       ^~~
/build/incubator-mxnet/3rdparty/dmlc-core/include/dmlc/././optional.h:56:7: warning: '*((void*)&<anonymous> +28)' may be used uninitialized in this function [-Wmaybe-uninitialized]
/build/incubator-mxnet/3rdparty/dmlc-core/include/dmlc/././optional.h:56:7: warning: '*((void*)&<anonymous> +36)' may be used uninitialized in this function [-Wmaybe-uninitialized]
[ 62%] Linking CXX static library libmxnet.a
[ 62%] Built target mxnet_static
make: *** [Makefile:141: all] Error 2
builder for '/nix/store/441s0xbzrha36xz9v8db2aa200ylwy5n-mxnet-1.2.0.drv' failed with exit code 2
cannot build derivation '/nix/store/q3bkkl9r9zikdk9j77dh9n2an0cr6vdb-python2.7-mxnet-1.2.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/74rzqx03va1avfkqv3i0x2lqla1ks6z1-python3.6-mxnet-1.2.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/74rzqx03va1avfkqv3i0x2lqla1ks6z1-python3.6-mxnet-1.2.0.drv', '/nix/store/q3bkkl9r9zikdk9j77dh9n2an0cr6vdb-python2.7-mxnet-1.2.0.drv' failed

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Timed out, unknown build status on x86_64-linux (full log)

Attempted: python2.pkgs.mxnet, python3.pkgs.mxnet

Partial log (click to expand)

shrinking /nix/store/rd8brnby987smf4282mr1cpzlxi4z470-python3.6-onnx-1.2.2/lib/python3.6/site-packages/onnx/onnx_cpp2py_export.cpython-36m-x86_64-linux-gnu.so
strip is /nix/store/gpc2wld1s0c6qzx9326cwn1wcx29xzsj-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/rd8brnby987smf4282mr1cpzlxi4z470-python3.6-onnx-1.2.2/lib  /nix/store/rd8brnby987smf4282mr1cpzlxi4z470-python3.6-onnx-1.2.2/bin
patching script interpreter paths in /nix/store/rd8brnby987smf4282mr1cpzlxi4z470-python3.6-onnx-1.2.2
checking for references to /build in /nix/store/rd8brnby987smf4282mr1cpzlxi4z470-python3.6-onnx-1.2.2...
wrapping `/nix/store/rd8brnby987smf4282mr1cpzlxi4z470-python3.6-onnx-1.2.2/bin/check-node'...
wrapping `/nix/store/rd8brnby987smf4282mr1cpzlxi4z470-python3.6-onnx-1.2.2/bin/backend-test-tools'...
wrapping `/nix/store/rd8brnby987smf4282mr1cpzlxi4z470-python3.6-onnx-1.2.2/bin/check-model'...
cannot build derivation '/nix/store/138sz5q73nwyh4dnni6sxabyyppqnw34-python3.6-mxnet-1.2.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/138sz5q73nwyh4dnni6sxabyyppqnw34-python3.6-mxnet-1.2.0.drv', '/nix/store/krqghg7gjv00sdrhwa6gywz5j6aj2n70-python2.7-mxnet-1.2.0.drv' failed

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@GrahamcOfBorg build python2.pkgs.mxnet python3.pkgs.mxnet

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No attempt on x86_64-darwin (full log)

The following builds were skipped because they don't evaluate on x86_64-darwin: python2.pkgs.mxnet, python3.pkgs.mxnet

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnsupportedSystem = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnsupportedSystem = true; }
to ~/.config/nixpkgs/config.nix.


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Failure on aarch64-linux (full log)

Attempted: python2.pkgs.mxnet, python3.pkgs.mxnet

Partial log (click to expand)

       ^~~
/build/incubator-mxnet/3rdparty/dmlc-core/include/dmlc/././optional.h:56:7: warning: '*((void*)&<anonymous> +28)' may be used uninitialized in this function [-Wmaybe-uninitialized]
/build/incubator-mxnet/3rdparty/dmlc-core/include/dmlc/././optional.h:56:7: warning: '*((void*)&<anonymous> +36)' may be used uninitialized in this function [-Wmaybe-uninitialized]
[ 62%] Linking CXX static library libmxnet.a
[ 62%] Built target mxnet_static
make: *** [Makefile:141: all] Error 2
builder for '/nix/store/441s0xbzrha36xz9v8db2aa200ylwy5n-mxnet-1.2.0.drv' failed with exit code 2
cannot build derivation '/nix/store/lpyc7kmqd4hq78k3q5fy4xn69d1lz77a-python2.7-mxnet-1.2.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/b5gqglpvb0f1jm1ks2226g44arnf4gh9-python3.6-mxnet-1.2.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/b5gqglpvb0f1jm1ks2226g44arnf4gh9-python3.6-mxnet-1.2.0.drv', '/nix/store/lpyc7kmqd4hq78k3q5fy4xn69d1lz77a-python2.7-mxnet-1.2.0.drv' failed

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Failure on x86_64-linux (full log)

Attempted: python2.pkgs.mxnet, python3.pkgs.mxnet

Partial log (click to expand)

shrinking /nix/store/rd8brnby987smf4282mr1cpzlxi4z470-python3.6-onnx-1.2.2/lib/python3.6/site-packages/onnx/onnx_cpp2py_export.cpython-36m-x86_64-linux-gnu.so
strip is /nix/store/gpc2wld1s0c6qzx9326cwn1wcx29xzsj-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/rd8brnby987smf4282mr1cpzlxi4z470-python3.6-onnx-1.2.2/lib  /nix/store/rd8brnby987smf4282mr1cpzlxi4z470-python3.6-onnx-1.2.2/bin
patching script interpreter paths in /nix/store/rd8brnby987smf4282mr1cpzlxi4z470-python3.6-onnx-1.2.2
checking for references to /build in /nix/store/rd8brnby987smf4282mr1cpzlxi4z470-python3.6-onnx-1.2.2...
wrapping `/nix/store/rd8brnby987smf4282mr1cpzlxi4z470-python3.6-onnx-1.2.2/bin/check-node'...
wrapping `/nix/store/rd8brnby987smf4282mr1cpzlxi4z470-python3.6-onnx-1.2.2/bin/backend-test-tools'...
wrapping `/nix/store/rd8brnby987smf4282mr1cpzlxi4z470-python3.6-onnx-1.2.2/bin/check-model'...
cannot build derivation '/nix/store/0lzbgf606ylip7zhk17vrbv6bib82yhf-python3.6-mxnet-1.2.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/0lzbgf606ylip7zhk17vrbv6bib82yhf-python3.6-mxnet-1.2.0.drv', '/nix/store/a650bizy0828wv4b7nk6v0nlrrmjjinf-python2.7-mxnet-1.2.0.drv' failed

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dotlambda commented Aug 12, 2018

/nix/store/gpc2wld1s0c6qzx9326cwn1wcx29xzsj-binutils-2.30/bin/ld: cannot find -llapack

Maybe there's a way to tell mxnet where to find liblapack?

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ttuegel commented Aug 12, 2018

Maybe there's a way to tell mxnet where to find liblapack?

It is included in libopenblas. You will need to tell mxnet to link libopenblas instead of libblas and liblapack.

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That's what I meant :)

@grwlf
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grwlf commented Aug 25, 2018

OK, I just go and fix it now :)

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grwlf commented Aug 25, 2018

@GrahamcOfBorg build python2.pkgs.mxnet python3.pkgs.mxnet

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Failure on aarch64-linux (full log)

Attempted: python2.pkgs.mxnet, python3.pkgs.mxnet

Partial log (click to expand)

wrapping `/nix/store/f46a0ymk2rrvy84b8yqqnj3dsy1qzlxh-python3.6-onnx-1.2.2/bin/check-node'...
wrapping `/nix/store/f46a0ymk2rrvy84b8yqqnj3dsy1qzlxh-python3.6-onnx-1.2.2/bin/check-model'...
wrapping `/nix/store/f46a0ymk2rrvy84b8yqqnj3dsy1qzlxh-python3.6-onnx-1.2.2/bin/backend-test-tools'...
[ 62%] Linking CXX static library libmxnet.a
[ 62%] Built target mxnet_static
make: *** [Makefile:141: all] Error 2
builder for '/nix/store/ikhnf36pac97vf1b7rjvmnzdgrj0d86b-mxnet-1.2.0.drv' failed with exit code 2
cannot build derivation '/nix/store/isgfwf12k2vk0wqxhdwwcsz3sjpa3g0c-python2.7-mxnet-1.2.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/1clggraq7nxlmgps6w8d9ma8bh9vfqdy-python3.6-mxnet-1.2.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/1clggraq7nxlmgps6w8d9ma8bh9vfqdy-python3.6-mxnet-1.2.0.drv', '/nix/store/isgfwf12k2vk0wqxhdwwcsz3sjpa3g0c-python2.7-mxnet-1.2.0.drv' failed

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grwlf commented Aug 25, 2018

/build/incubator-mxnet/3rdparty/mkldnn/src/cpu/xbyak/xbyak_util.h:84:12: fatal error: cpuid.h: No such file or directory
   #include <cpuid.h>
            ^~~~~~~~~

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Failure on aarch64-linux (full log)

Attempted: mxnet

Partial log (click to expand)

/build/incubator-mxnet/3rdparty/dmlc-core/include/dmlc/././optional.h:56:7: warning: '*((void*)&<anonymous> +20)' may be used uninitialized in this function [-Wmaybe-uninitialized]
       new (&val) T(other.value());
       ^~~
/build/incubator-mxnet/3rdparty/dmlc-core/include/dmlc/././optional.h:56:7: warning: '*((void*)&<anonymous> +28)' may be used uninitialized in this function [-Wmaybe-uninitialized]
/build/incubator-mxnet/3rdparty/dmlc-core/include/dmlc/././optional.h:56:7: warning: '*((void*)&<anonymous> +36)' may be used uninitialized in this function [-Wmaybe-uninitialized]
[ 62%] Linking CXX static library libmxnet.a
[ 62%] Built target mxnet_static
make: *** [Makefile:141: all] Error 2
builder for '/nix/store/ikhnf36pac97vf1b7rjvmnzdgrj0d86b-mxnet-1.2.0.drv' failed with exit code 2
error: build of '/nix/store/ikhnf36pac97vf1b7rjvmnzdgrj0d86b-mxnet-1.2.0.drv' failed

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Timed out, unknown build status on x86_64-linux (full log)

Attempted: mxnet

Partial log (click to expand)

/build/incubator-mxnet/3rdparty/dmlc-core/include/dmlc/././optional.h:56:7: warning: '*((void*)&<anonymous> +28)' may be used uninitialized in this function [-Wmaybe-uninitialized]
/build/incubator-mxnet/3rdparty/dmlc-core/include/dmlc/././optional.h:56:7: warning: '*((void*)&<anonymous> +36)' may be used uninitialized in this function [-Wmaybe-uninitialized]
[ 90%] Building CXX object CMakeFiles/mxnet_static.dir/src/operator/tensor/ordering_op.cc.o
[ 91%] Building CXX object CMakeFiles/mxnet_static.dir/src/operator/tensor/sparse_retain.cc.o
[ 91%] Building CXX object CMakeFiles/mxnet_static.dir/src/operator/tensor/square_sum.cc.o
[ 91%] Building CXX object CMakeFiles/mxnet_static.dir/src/profiler/aggregate_stats.cc.o
[ 91%] Building CXX object CMakeFiles/mxnet_static.dir/src/profiler/profiler.cc.o
[ 91%] Building CXX object CMakeFiles/mxnet_static.dir/src/profiler/vtune.cc.o
building of '/nix/store/fbnm67d0q3ivzz3zsjspiw7wivgczsqv-mxnet-1.2.0.drv' timed out after 1800 seconds
error: build of '/nix/store/fbnm67d0q3ivzz3zsjspiw7wivgczsqv-mxnet-1.2.0.drv' failed

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Timed out, unknown build status on x86_64-linux (full log)

Attempted: python2.pkgs.mxnet, python3.pkgs.mxnet

Partial log (click to expand)

[ 32%] Building CXX object CMakeFiles/mxnet_static.dir/src/operator/tensor/elemwise_binary_op.cc.o
[ 32%] Building CXX object CMakeFiles/mxnet_static.dir/src/operator/tensor/elemwise_binary_op_basic.cc.o
[ 33%] Building CXX object CMakeFiles/mxnet_static.dir/src/operator/tensor/elemwise_binary_op_extended.cc.o
[ 33%] Building CXX object CMakeFiles/mxnet_static.dir/src/operator/tensor/elemwise_binary_op_logic.cc.o
[ 33%] Building CXX object CMakeFiles/mxnet_static.dir/src/operator/tensor/elemwise_binary_scalar_op_basic.cc.o
[ 33%] Building CXX object CMakeFiles/mxnet_static.dir/src/operator/tensor/elemwise_binary_scalar_op_extended.cc.o
building of '/nix/store/fbnm67d0q3ivzz3zsjspiw7wivgczsqv-mxnet-1.2.0.drv' timed out after 3600 seconds
cannot build derivation '/nix/store/7cb0736icrjmsrh1m94g5q44fgnfydi8-python2.7-mxnet-1.2.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/5ww6ddajb9n6dygqs5wyjm7cbyhs147y-python3.6-mxnet-1.2.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/5ww6ddajb9n6dygqs5wyjm7cbyhs147y-python3.6-mxnet-1.2.0.drv', '/nix/store/7cb0736icrjmsrh1m94g5q44fgnfydi8-python2.7-mxnet-1.2.0.drv' failed

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grwlf commented Aug 25, 2018

@GrahamcOfBorg build python2.pkgs.mxnet python3.pkgs.mxnet

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Failure on x86_64-linux (full log)

Attempted: python2.pkgs.mxnet, python3.pkgs.mxnet

Partial log (click to expand)

shrinking /nix/store/6y65h640bn1smcrn5i7z2z4n4l2ryfc6-python3.6-onnx-1.2.2/lib/python3.6/site-packages/onnx/onnx_cpp2py_export.cpython-36m-x86_64-linux-gnu.so
strip is /nix/store/h0lbngpv6ln56hjj59i6l77vxq25flbz-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/6y65h640bn1smcrn5i7z2z4n4l2ryfc6-python3.6-onnx-1.2.2/lib  /nix/store/6y65h640bn1smcrn5i7z2z4n4l2ryfc6-python3.6-onnx-1.2.2/bin
patching script interpreter paths in /nix/store/6y65h640bn1smcrn5i7z2z4n4l2ryfc6-python3.6-onnx-1.2.2
checking for references to /build in /nix/store/6y65h640bn1smcrn5i7z2z4n4l2ryfc6-python3.6-onnx-1.2.2...
wrapping `/nix/store/6y65h640bn1smcrn5i7z2z4n4l2ryfc6-python3.6-onnx-1.2.2/bin/check-node'...
wrapping `/nix/store/6y65h640bn1smcrn5i7z2z4n4l2ryfc6-python3.6-onnx-1.2.2/bin/backend-test-tools'...
wrapping `/nix/store/6y65h640bn1smcrn5i7z2z4n4l2ryfc6-python3.6-onnx-1.2.2/bin/check-model'...
cannot build derivation '/nix/store/5ww6ddajb9n6dygqs5wyjm7cbyhs147y-python3.6-mxnet-1.2.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/5ww6ddajb9n6dygqs5wyjm7cbyhs147y-python3.6-mxnet-1.2.0.drv', '/nix/store/7cb0736icrjmsrh1m94g5q44fgnfydi8-python2.7-mxnet-1.2.0.drv' failed

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Failure on aarch64-linux (full log)

Attempted: python2.pkgs.mxnet, python3.pkgs.mxnet

Partial log (click to expand)

       ^~~
/build/incubator-mxnet/3rdparty/dmlc-core/include/dmlc/././optional.h:56:7: warning: '*((void*)&<anonymous> +28)' may be used uninitialized in this function [-Wmaybe-uninitialized]
/build/incubator-mxnet/3rdparty/dmlc-core/include/dmlc/././optional.h:56:7: warning: '*((void*)&<anonymous> +36)' may be used uninitialized in this function [-Wmaybe-uninitialized]
[ 62%] Linking CXX static library libmxnet.a
[ 62%] Built target mxnet_static
make: *** [Makefile:141: all] Error 2
builder for '/nix/store/ikhnf36pac97vf1b7rjvmnzdgrj0d86b-mxnet-1.2.0.drv' failed with exit code 2
cannot build derivation '/nix/store/isgfwf12k2vk0wqxhdwwcsz3sjpa3g0c-python2.7-mxnet-1.2.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/1clggraq7nxlmgps6w8d9ma8bh9vfqdy-python3.6-mxnet-1.2.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/1clggraq7nxlmgps6w8d9ma8bh9vfqdy-python3.6-mxnet-1.2.0.drv', '/nix/store/isgfwf12k2vk0wqxhdwwcsz3sjpa3g0c-python2.7-mxnet-1.2.0.drv' failed

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grwlf commented Sep 23, 2018

It was too hard. Obsolete now :(

@grwlf grwlf closed this Sep 23, 2018
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6 participants