[WIP] pythonPackages.cvxopt: fix transient test failure #42918

timokau · 2018-07-03T15:19:56Z

Motivation for this change

For some reason after the openblas 3.0.1 update
(c8ed322), cvxopt fails to build with
the pinned glpk. Removing that dependency override fixes that. Its not
very pretty because now sage depends on 2 different glpk versions. But
it should be enough until the next glpk update, which will make the glpk
pinning unnecessary (https://trac.sagemath.org/ticket/24824).

I have really no clue how a minor version update in openblas made the build (test) of cvxopt fail, but who understands computers anymore anyhow...

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.

timokau · 2018-07-03T15:20:43Z

Another try:
@GrahamcOfBorg build sage.lib

GrahamcOfBorg · 2018-07-03T15:21:03Z

No attempt on x86_64-darwin (full log)

The following builds were skipped because they don't evaluate on x86_64-darwin: sage.lib

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.

GrahamcOfBorg · 2018-07-03T15:39:19Z

No attempt on x86_64-darwin (full log)

The following builds were skipped because they don't evaluate on x86_64-darwin: sage

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.

GrahamcOfBorg · 2018-07-03T15:39:36Z

No attempt on aarch64-linux (full log)

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

Partial log (click to expand)


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

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

GrahamcOfBorg · 2018-07-03T15:42:09Z

Success on x86_64-linux (full log)

Attempted: sage.lib

Partial log (click to expand)

shrinking /nix/store/7xnvcgf22cd7alv48fwary42smbh8554-python2.7-sagelib-8.2/lib/python2.7/site-packages/sage/rings/finite_rings/element_base.so
shrinking /nix/store/7xnvcgf22cd7alv48fwary42smbh8554-python2.7-sagelib-8.2/lib/python2.7/site-packages/sage/rings/finite_rings/hom_finite_field.so
shrinking /nix/store/7xnvcgf22cd7alv48fwary42smbh8554-python2.7-sagelib-8.2/lib/python2.7/site-packages/sage/rings/finite_rings/finite_field_base.so
shrinking /nix/store/7xnvcgf22cd7alv48fwary42smbh8554-python2.7-sagelib-8.2/lib/python2.7/site-packages/sage/rings/finite_rings/hom_finite_field_givaro.so
shrinking /nix/store/7xnvcgf22cd7alv48fwary42smbh8554-python2.7-sagelib-8.2/lib/python2.7/site-packages/sage/functions/prime_pi.so
strip is /nix/store/4qvrxzxa535y8304mk195x50b6p9607d-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/7xnvcgf22cd7alv48fwary42smbh8554-python2.7-sagelib-8.2/lib
patching script interpreter paths in /nix/store/7xnvcgf22cd7alv48fwary42smbh8554-python2.7-sagelib-8.2
checking for references to /build in /nix/store/7xnvcgf22cd7alv48fwary42smbh8554-python2.7-sagelib-8.2...
/nix/store/7xnvcgf22cd7alv48fwary42smbh8554-python2.7-sagelib-8.2

GrahamcOfBorg · 2018-07-03T15:47:34Z

Failure on x86_64-linux (full log)

Attempted: sage

Partial log (click to expand)

shrinking RPATHs of ELF executables and libraries in /nix/store/bpwgxg99z97r9ldhpl6vkjflpfg8igdb-R-3.4.4-wrapper
strip is /nix/store/4qvrxzxa535y8304mk195x50b6p9607d-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/bpwgxg99z97r9ldhpl6vkjflpfg8igdb-R-3.4.4-wrapper/bin
patching script interpreter paths in /nix/store/bpwgxg99z97r9ldhpl6vkjflpfg8igdb-R-3.4.4-wrapper
checking for references to /build in /nix/store/bpwgxg99z97r9ldhpl6vkjflpfg8igdb-R-3.4.4-wrapper...
cannot build derivation '/nix/store/ppfpccxlwp741h3a1rrvqyr48g9dr6b3-sage-env.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/kkvik4kzg19nz08yasiii3cnr3c1rjnn-sage-with-env-8.2.drv': 2 dependencies couldn't be built
cannot build derivation '/nix/store/ra2hzpvpqiv1nhim8n56jhkvv2cxz3yf-sage-8.2.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/ryb3p9myhm3sc053az7i8dfwl97v52dh-sage-wrapper-8.2.drv': 1 dependencies couldn't be built
error: build of '/nix/store/ryb3p9myhm3sc053az7i8dfwl97v52dh-sage-wrapper-8.2.drv' failed

timokau · 2018-07-03T16:01:46Z

Good to know sage.lib fits ofBorgs timelimit :)

Apparently the cause for the error made no sense because it was not actually the cause of the error (see sage ofBorg log). It did fix it locally for me though, so probably some transient error. I'll have to investigate.

GrahamcOfBorg · 2018-07-03T16:47:42Z

Failure on aarch64-linux (full log)

Attempted: sage.lib

Partial log (click to expand)

shrinking /nix/store/xw4nv1kqjh6fyfm8sv9583f770qn4yix-eclib-20171219/bin/solve_legendre
shrinking /nix/store/xw4nv1kqjh6fyfm8sv9583f770qn4yix-eclib-20171219/bin/solve_conic
shrinking /nix/store/xw4nv1kqjh6fyfm8sv9583f770qn4yix-eclib-20171219/lib/libec.so.4.0.0
gzipping man pages under /nix/store/xw4nv1kqjh6fyfm8sv9583f770qn4yix-eclib-20171219/share/man/
strip is /nix/store/0pjsgkxz0rp5baycq5sp2s72lrr5q9sg-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/xw4nv1kqjh6fyfm8sv9583f770qn4yix-eclib-20171219/lib  /nix/store/xw4nv1kqjh6fyfm8sv9583f770qn4yix-eclib-20171219/bin
patching script interpreter paths in /nix/store/xw4nv1kqjh6fyfm8sv9583f770qn4yix-eclib-20171219
checking for references to /build in /nix/store/xw4nv1kqjh6fyfm8sv9583f770qn4yix-eclib-20171219...
cannot build derivation '/nix/store/5f9gfbd94jyb50dsw2zs52z3iqnkd63g-python2.7-sagelib-8.2.drv': 4 dependencies couldn't be built
error: build of '/nix/store/5f9gfbd94jyb50dsw2zs52z3iqnkd63g-python2.7-sagelib-8.2.drv' failed

timokau · 2018-07-03T17:10:54Z

Quick update: This is a transient test failure of cvxopt and apparently was introduced by (my) commit 156e910, "pythonPackages.cvxopt: 1.1.7 -> 1.1.9" in which I also added glpk, gsl and fftw support. One of those is probably responsible, maybe cvxopt/cvxopt#120 is relevant (I basically only read the title).

I don't have any time to continue right now. So in case anybody else feels like it, go ahead.

timokau · 2018-07-05T13:39:47Z

This took way longer to track down than I'd like to admit. Turns out using openblas for lapack causes the error. Reported upstream here: cvxopt/cvxopt#122

Depending on how fast (and if) upstream fixes the issue I'll backport the fix or switch to liblapack. I'd rather backport the switch though, because IIRC liblapack depends on atlas which takes forever to build.

timokau · 2018-07-06T16:55:56Z

It looks like it might take a while to fix upstream. Switching to liblapack for now.

@GrahamcOfBorg build python2.pkgs.cvxopt
@GrahamcOfBorg build python3.pkgs.cvxopt

GrahamcOfBorg · 2018-07-06T16:56:51Z

Failure on aarch64-linux (full log)

Attempted: python3.pkgs.cvxopt

Partial log (click to expand)

../configure: line 484: can't create lib/Makefile: nonexistent directory
../configure: line 485: can't create lib/Makefile: nonexistent directory
../configure: line 541: can't create lib/Makefile: nonexistent directory
DONE configure
/nix/store/s7p3hkplihq7g4njaq1gn77id2bn2aqm-stdenv-linux/setup: line 100: include/atlas_cacheedge.h: No such file or directory
builder for '/nix/store/c20djyii5jdq1w4f1jpgdk9k3j4m8xqp-atlas-3.10.3.drv' failed with exit code 1
cannot build derivation '/nix/store/h3lgi4hksrh02pc4w5p1fbmdjvg526bf-liblapack-3.8.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/05x5jqq31ym7faj6xipp5qc52l2xb1v2-openblas-liblapack-join.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/h4gsrs8ss8axsb3z1741k7xnw73z5nak-python3.6-cvxopt-1.2.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/h4gsrs8ss8axsb3z1741k7xnw73z5nak-python3.6-cvxopt-1.2.0.drv' failed

GrahamcOfBorg · 2018-07-06T16:57:11Z

Failure on aarch64-linux (full log)

Attempted: python2.pkgs.cvxopt

Partial log (click to expand)

../configure: line 484: can't create lib/Makefile: nonexistent directory
../configure: line 485: can't create lib/Makefile: nonexistent directory
../configure: line 541: can't create lib/Makefile: nonexistent directory
DONE configure
/nix/store/s7p3hkplihq7g4njaq1gn77id2bn2aqm-stdenv-linux/setup: line 100: include/atlas_cacheedge.h: No such file or directory
builder for '/nix/store/c20djyii5jdq1w4f1jpgdk9k3j4m8xqp-atlas-3.10.3.drv' failed with exit code 1
cannot build derivation '/nix/store/h3lgi4hksrh02pc4w5p1fbmdjvg526bf-liblapack-3.8.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/05x5jqq31ym7faj6xipp5qc52l2xb1v2-openblas-liblapack-join.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/7wpff0mnxwcb129j9kzcv5jf7pm5ai3y-python2.7-cvxopt-1.2.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/7wpff0mnxwcb129j9kzcv5jf7pm5ai3y-python2.7-cvxopt-1.2.0.drv' failed

GrahamcOfBorg · 2018-07-06T16:57:12Z

Success on x86_64-linux (full log)

Attempted: python3.pkgs.cvxopt

Partial log (click to expand)

21: -3.1605e+02 -3.1621e+02  2e+00  4e-06  3e-04  5e-03
22: -3.1548e+02 -3.1553e+02  7e-01  1e-06  8e-05  1e-03
23: -3.1537e+02 -3.1540e+02  5e-01  7e-07  5e-05  9e-04
24: -3.1536e+02 -3.1540e+02  9e-01  9e-07  7e-05  2e-03
25: -3.1533e+02 -3.1536e+02  5e-01  7e-07  6e-05  1e-03
26: -3.1515e+02 -3.1517e+02  3e-01  3e-07  2e-05  7e-04
27: -3.1503e+02 -3.1504e+02  3e-02  3e-08  2e-06  8e-05
28: -3.1502e+02 -3.1502e+02  3e-04  3e-10  3e-08  8e-07
29: -3.1502e+02 -3.1502e+02  3e-06  3e-12  3e-10  8e-09
Optimal solution found.

GrahamcOfBorg · 2018-07-06T16:57:28Z

Success on x86_64-linux (full log)

Attempted: python2.pkgs.cvxopt

Partial log (click to expand)

 h = 2.887313,  w = 5.774627, d = 11.542511.

     pcost       dcost       gap    pres   dres
 0:  0.0000e+00  6.2127e+04  1e+00  1e+00  1e+00
 1: -6.1389e+04  6.7930e+01  1e-02  1e+00  1e-02
 2: -5.5922e+02  6.1534e+01  1e-04  1e-02  1e-04
 3:  5.5319e+01  6.1530e+01  1e-06  1e-04  1e-06
 4:  6.1468e+01  6.1530e+01  1e-08  1e-06  1e-08
 5:  6.1530e+01  6.1530e+01  1e-10  1e-08  1e-10
Optimal solution found.

See cvxopt/cvxopt#122 for more info.

timokau · 2018-07-06T17:03:22Z

@GrahamcOfBorg build python2.pkgs.cvxopt
@GrahamcOfBorg build python3.pkgs.cvxopt

GrahamcOfBorg · 2018-07-06T17:03:52Z

Success on x86_64-linux (full log)

Attempted: python2.pkgs.cvxopt

Partial log (click to expand)

Long-step dual simplex will be used
+     0: mip =     not found yet >=              -inf        (1; 0)
+     0: >>>>>  -5.000000000e+00 >=  -5.000000000e+00   0.0% (1; 0)
+     0: mip =  -5.000000000e+00 >=     tree is empty   0.0% (0; 1)
INTEGER OPTIMAL SOLUTION FOUND
....
----------------------------------------------------------------------
Ran 38 tests in 3.210s

OK (skipped=6)

timokau · 2018-07-06T17:04:09Z

Oh damn forgot to push first.
@GrahamcOfBorg build python2.pkgs.cvxopt
@GrahamcOfBorg build python3.pkgs.cvxopt

GrahamcOfBorg · 2018-07-06T17:04:15Z

Failure on aarch64-linux (full log)

Attempted: python3.pkgs.cvxopt

Partial log (click to expand)

../configure: line 484: can't create lib/Makefile: nonexistent directory
../configure: line 485: can't create lib/Makefile: nonexistent directory
../configure: line 541: can't create lib/Makefile: nonexistent directory
DONE configure
/nix/store/s7p3hkplihq7g4njaq1gn77id2bn2aqm-stdenv-linux/setup: line 100: include/atlas_cacheedge.h: No such file or directory
builder for '/nix/store/c20djyii5jdq1w4f1jpgdk9k3j4m8xqp-atlas-3.10.3.drv' failed with exit code 1
cannot build derivation '/nix/store/h3lgi4hksrh02pc4w5p1fbmdjvg526bf-liblapack-3.8.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/05x5jqq31ym7faj6xipp5qc52l2xb1v2-openblas-liblapack-join.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/h4gsrs8ss8axsb3z1741k7xnw73z5nak-python3.6-cvxopt-1.2.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/h4gsrs8ss8axsb3z1741k7xnw73z5nak-python3.6-cvxopt-1.2.0.drv' failed

GrahamcOfBorg · 2018-07-06T17:04:35Z

Failure on aarch64-linux (full log)

Attempted: python2.pkgs.cvxopt

Partial log (click to expand)

../configure: line 484: can't create lib/Makefile: nonexistent directory
../configure: line 485: can't create lib/Makefile: nonexistent directory
../configure: line 541: can't create lib/Makefile: nonexistent directory
DONE configure
/nix/store/s7p3hkplihq7g4njaq1gn77id2bn2aqm-stdenv-linux/setup: line 100: include/atlas_cacheedge.h: No such file or directory
builder for '/nix/store/c20djyii5jdq1w4f1jpgdk9k3j4m8xqp-atlas-3.10.3.drv' failed with exit code 1
cannot build derivation '/nix/store/h3lgi4hksrh02pc4w5p1fbmdjvg526bf-liblapack-3.8.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/05x5jqq31ym7faj6xipp5qc52l2xb1v2-openblas-liblapack-join.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/7wpff0mnxwcb129j9kzcv5jf7pm5ai3y-python2.7-cvxopt-1.2.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/7wpff0mnxwcb129j9kzcv5jf7pm5ai3y-python2.7-cvxopt-1.2.0.drv' failed

GrahamcOfBorg · 2018-07-06T17:04:37Z

Success on x86_64-linux (full log)

Attempted: python3.pkgs.cvxopt

Partial log (click to expand)

21: -3.1605e+02 -3.1621e+02  2e+00  4e-06  3e-04  5e-03
22: -3.1548e+02 -3.1553e+02  7e-01  1e-06  8e-05  1e-03
23: -3.1537e+02 -3.1540e+02  5e-01  7e-07  5e-05  9e-04
24: -3.1536e+02 -3.1540e+02  9e-01  9e-07  7e-05  2e-03
25: -3.1533e+02 -3.1536e+02  5e-01  7e-07  6e-05  1e-03
26: -3.1515e+02 -3.1517e+02  3e-01  3e-07  2e-05  7e-04
27: -3.1503e+02 -3.1504e+02  3e-02  3e-08  2e-06  8e-05
28: -3.1502e+02 -3.1502e+02  3e-04  3e-10  3e-08  8e-07
29: -3.1502e+02 -3.1502e+02  3e-06  3e-12  3e-10  8e-09
Optimal solution found.

GrahamcOfBorg · 2018-07-06T17:04:41Z

Success on x86_64-linux (full log)

Attempted: python2.pkgs.cvxopt

Partial log (click to expand)

Long-step dual simplex will be used
+     0: mip =     not found yet >=              -inf        (1; 0)
+     0: >>>>>  -5.000000000e+00 >=  -5.000000000e+00   0.0% (1; 0)
+     0: mip =  -5.000000000e+00 >=     tree is empty   0.0% (0; 1)
INTEGER OPTIMAL SOLUTION FOUND
....
----------------------------------------------------------------------
Ran 38 tests in 3.070s

OK (skipped=6)

GrahamcOfBorg · 2018-07-06T17:05:00Z

Failure on aarch64-linux (full log)

Attempted: python3.pkgs.cvxopt

Partial log (click to expand)

../configure: line 484: can't create lib/Makefile: nonexistent directory
../configure: line 485: can't create lib/Makefile: nonexistent directory
../configure: line 541: can't create lib/Makefile: nonexistent directory
DONE configure
/nix/store/s7p3hkplihq7g4njaq1gn77id2bn2aqm-stdenv-linux/setup: line 100: include/atlas_cacheedge.h: No such file or directory
builder for '/nix/store/c20djyii5jdq1w4f1jpgdk9k3j4m8xqp-atlas-3.10.3.drv' failed with exit code 1
cannot build derivation '/nix/store/h3lgi4hksrh02pc4w5p1fbmdjvg526bf-liblapack-3.8.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/05x5jqq31ym7faj6xipp5qc52l2xb1v2-openblas-liblapack-join.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/nrdb9kwwljs0rrdhd6jbihqh3fincqgh-python3.6-cvxopt-1.2.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/nrdb9kwwljs0rrdhd6jbihqh3fincqgh-python3.6-cvxopt-1.2.0.drv' failed

GrahamcOfBorg · 2018-07-06T17:05:20Z

Failure on aarch64-linux (full log)

Attempted: python2.pkgs.cvxopt

Partial log (click to expand)

../configure: line 484: can't create lib/Makefile: nonexistent directory
../configure: line 485: can't create lib/Makefile: nonexistent directory
../configure: line 541: can't create lib/Makefile: nonexistent directory
DONE configure
/nix/store/s7p3hkplihq7g4njaq1gn77id2bn2aqm-stdenv-linux/setup: line 100: include/atlas_cacheedge.h: No such file or directory
builder for '/nix/store/c20djyii5jdq1w4f1jpgdk9k3j4m8xqp-atlas-3.10.3.drv' failed with exit code 1
cannot build derivation '/nix/store/h3lgi4hksrh02pc4w5p1fbmdjvg526bf-liblapack-3.8.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/05x5jqq31ym7faj6xipp5qc52l2xb1v2-openblas-liblapack-join.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/fq8ngn4nr4hr88bylcl37bq168wds13h-python2.7-cvxopt-1.2.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/fq8ngn4nr4hr88bylcl37bq168wds13h-python2.7-cvxopt-1.2.0.drv' failed

GrahamcOfBorg · 2018-07-06T17:05:52Z

Success on x86_64-linux (full log)

Attempted: python3.pkgs.cvxopt

Partial log (click to expand)

21: -3.1605e+02 -3.1621e+02  2e+00  4e-06  3e-04  5e-03
22: -3.1548e+02 -3.1553e+02  7e-01  1e-06  8e-05  1e-03
23: -3.1537e+02 -3.1540e+02  5e-01  7e-07  5e-05  9e-04
24: -3.1536e+02 -3.1540e+02  9e-01  9e-07  7e-05  2e-03
25: -3.1533e+02 -3.1536e+02  5e-01  7e-07  6e-05  1e-03
26: -3.1515e+02 -3.1517e+02  3e-01  3e-07  2e-05  7e-04
27: -3.1503e+02 -3.1504e+02  3e-02  3e-08  2e-06  8e-05
28: -3.1502e+02 -3.1502e+02  3e-04  3e-10  3e-08  8e-07
29: -3.1502e+02 -3.1502e+02  3e-06  3e-12  3e-10  8e-09
Optimal solution found.

timokau · 2018-07-06T17:08:59Z

Looks like that doesn't actually fix the problem...

Edit: The test error is very enlightening

Traceback (most recent call last):
  File "/tmp/nix-build-python2.7-cvxopt-1.2.0.drv-0/cvxopt-1.2.0/tests/test_modeling.py", line 57, in test_case3
    self.assertTrue(lp3.status == 'optimal')
AssertionError: False is not true

GrahamcOfBorg · 2018-07-06T17:26:23Z

Failure on x86_64-darwin (full log)

Attempted: python2.pkgs.cvxopt

Partial log (click to expand)

/nix/store/1amqnm1g8088dj1nn349x75pdbwff99h-gfortran-wrapper-7.3.0/bin/gcc -DL2SIZE=33554432 -I/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/include -I/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/..//include -I/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX -DATL_ARCH_IBMz13 -DATL_SSE3 -DATL_SSE2 -DATL_USE64BITS -m64  -O -fomit-frame-pointer -msse3 -m64 -o xemit_lamch emit_lamch.o -lm
/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/bin/ATLrun.sh /private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/tune/sysinfo xemit_lamch
cp res/atlas_?lamch.h /private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/include/.
make[3]: Leaving directory '/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/tune/sysinfo'
make[2]: Leaving directory '/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/bin'
building of '/nix/store/8738r52can3dwx2crgbzxbd6i2whip9r-atlas-3.10.3.drv' timed out after 1800 seconds
cannot build derivation '/nix/store/mjmsqf8v1bn0v4c4mdrwvimdpilnk6a6-liblapack-3.8.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/9yk0gicww0ixxm6l0f4pfmjkqljlpg7w-openblas-liblapack-join.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/k7hjnlkh5jvzdvbrhrcwvm6igy290hph-python2.7-cvxopt-1.2.0.drv': 1 dependencies couldn't be built
�[31;1merror:�[0m build of '/nix/store/k7hjnlkh5jvzdvbrhrcwvm6igy290hph-python2.7-cvxopt-1.2.0.drv' failed

GrahamcOfBorg · 2018-07-06T17:56:15Z

Failure on x86_64-darwin (full log)

Attempted: python3.pkgs.cvxopt

Partial log (click to expand)

clang-5.0: warning: argument unused during compilation: '--param ssp-buffer-size=4' [-Wunused-command-line-argument]
clang-5.0: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument]
clang-5.0: warning: argument unused during compilation: '-idirafter /nix/store/q819d3vjz7vswpvkrfa9gck3ys8rmvcj-Libsystem-osx-10.11.6/include' [-Wunused-command-line-argument]
clang-5.0: warning: argument unused during compilation: '-idirafter /nix/store/lxqad4yxznyd27v5sdz5jrazvqyjlay4-gfortran-7.3.0/lib/gcc/x86_64-apple-darwin/7.3.0/include-fixed' [-Wunused-command-line-argument]
clang-5.0: warning: argument unused during compilation: '-isystem /nix/store/cssxc3nfsvn3a88dsdjx0wr8wq61xv4v-libc++-5.0.2/include' [-Wunused-command-line-argument]
building of '/nix/store/8738r52can3dwx2crgbzxbd6i2whip9r-atlas-3.10.3.drv' timed out after 1800 seconds
cannot build derivation '/nix/store/mjmsqf8v1bn0v4c4mdrwvimdpilnk6a6-liblapack-3.8.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/9yk0gicww0ixxm6l0f4pfmjkqljlpg7w-openblas-liblapack-join.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/r9qfj7kjmyx7kcwxdixcgk9r6yy2qxvx-python3.6-cvxopt-1.2.0.drv': 1 dependencies couldn't be built
�[31;1merror:�[0m build of '/nix/store/r9qfj7kjmyx7kcwxdixcgk9r6yy2qxvx-python3.6-cvxopt-1.2.0.drv' failed

GrahamcOfBorg · 2018-07-06T19:07:11Z

Failure on x86_64-darwin (full log)

Attempted: python2.pkgs.cvxopt

Partial log (click to expand)

/nix/store/1amqnm1g8088dj1nn349x75pdbwff99h-gfortran-wrapper-7.3.0/bin/gcc -DL2SIZE=33554432 -I/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/include -I/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/..//include -I/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX -DATL_ARCH_IBMz13 -DATL_SSE3 -DATL_SSE2 -DATL_USE64BITS -m64  -O -fomit-frame-pointer -msse3 -m64 -o xemit_lamch emit_lamch.o -lm
/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/bin/ATLrun.sh /private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/tune/sysinfo xemit_lamch
cp res/atlas_?lamch.h /private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/include/.
make[3]: Leaving directory '/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/tune/sysinfo'
make[2]: Leaving directory '/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/bin'
building of '/nix/store/8738r52can3dwx2crgbzxbd6i2whip9r-atlas-3.10.3.drv' timed out after 1800 seconds
cannot build derivation '/nix/store/mjmsqf8v1bn0v4c4mdrwvimdpilnk6a6-liblapack-3.8.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/9yk0gicww0ixxm6l0f4pfmjkqljlpg7w-openblas-liblapack-join.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/k7hjnlkh5jvzdvbrhrcwvm6igy290hph-python2.7-cvxopt-1.2.0.drv': 1 dependencies couldn't be built
�[31;1merror:�[0m build of '/nix/store/k7hjnlkh5jvzdvbrhrcwvm6igy290hph-python2.7-cvxopt-1.2.0.drv' failed

GrahamcOfBorg · 2018-07-06T19:37:02Z

Failure on x86_64-darwin (full log)

Attempted: python3.pkgs.cvxopt

Partial log (click to expand)

/nix/store/1amqnm1g8088dj1nn349x75pdbwff99h-gfortran-wrapper-7.3.0/bin/gcc -DL2SIZE=33554432 -I/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/include -I/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/..//include -I/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX -DATL_ARCH_IBMz13 -DATL_SSE3 -DATL_SSE2 -DATL_USE64BITS -m64  -O -fomit-frame-pointer -msse3 -m64 -o xemit_lamch emit_lamch.o -lm
/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/bin/ATLrun.sh /private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/tune/sysinfo xemit_lamch
cp res/atlas_?lamch.h /private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/include/.
make[3]: Leaving directory '/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/tune/sysinfo'
make[2]: Leaving directory '/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/bin'
building of '/nix/store/8738r52can3dwx2crgbzxbd6i2whip9r-atlas-3.10.3.drv' timed out after 1800 seconds
cannot build derivation '/nix/store/mjmsqf8v1bn0v4c4mdrwvimdpilnk6a6-liblapack-3.8.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/9yk0gicww0ixxm6l0f4pfmjkqljlpg7w-openblas-liblapack-join.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/r9qfj7kjmyx7kcwxdixcgk9r6yy2qxvx-python3.6-cvxopt-1.2.0.drv': 1 dependencies couldn't be built
�[31;1merror:�[0m build of '/nix/store/r9qfj7kjmyx7kcwxdixcgk9r6yy2qxvx-python3.6-cvxopt-1.2.0.drv' failed

GrahamcOfBorg · 2018-07-06T20:07:32Z

Failure on x86_64-darwin (full log)

Attempted: python2.pkgs.cvxopt

Partial log (click to expand)

clang-5.0: warning: argument unused during compilation: '-isystem /nix/store/cssxc3nfsvn3a88dsdjx0wr8wq61xv4v-libc++-5.0.2/include' [-Wunused-command-line-argument]
clang-5.0: warning: argument unused during compilation: '-isystem /nix/store/610adibjkd5h07niii5q0si6kc6cgca1-libc++abi-5.0.2/include' [-Wunused-command-line-argument]
clang-5.0: warning: argument unused during compilation: '-isystem /nix/store/ika0jc7pka2gp485jn4d6har92ycyrxb-compiler-rt-5.0.2-dev/include' [-Wunused-command-line-argument]
clang-5.0: warning: argument unused during compilation: '-F/nix/store/shgpngxlby2rw80wbacswld028b61cj7-CF-osx-10.10.5/Library/Frameworks' [-Wunused-command-line-argument]
clang-5.0: warning: argument unused during compilation: '-isystem /nix/store/cssxc3nfsvn3a88dsdjx0wr8wq61xv4v-libc++-5.0.2/include' [-Wunused-command-line-argument]
building of '/nix/store/8738r52can3dwx2crgbzxbd6i2whip9r-atlas-3.10.3.drv' timed out after 1800 seconds
cannot build derivation '/nix/store/mjmsqf8v1bn0v4c4mdrwvimdpilnk6a6-liblapack-3.8.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/9yk0gicww0ixxm6l0f4pfmjkqljlpg7w-openblas-liblapack-join.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/8k3i8jh2sh9sw69r03m4lg34hawrzklz-python2.7-cvxopt-1.2.0.drv': 1 dependencies couldn't be built
�[31;1merror:�[0m build of '/nix/store/8k3i8jh2sh9sw69r03m4lg34hawrzklz-python2.7-cvxopt-1.2.0.drv' failed

GrahamcOfBorg · 2018-07-06T20:37:57Z

Failure on x86_64-darwin (full log)

Attempted: python3.pkgs.cvxopt

Partial log (click to expand)

/nix/store/1amqnm1g8088dj1nn349x75pdbwff99h-gfortran-wrapper-7.3.0/bin/gcc -DL2SIZE=33554432 -I/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/include -I/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/..//include -I/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX -DATL_ARCH_IBMz13 -DATL_SSE3 -DATL_SSE2 -DATL_USE64BITS -m64  -O -fomit-frame-pointer -msse3 -m64 -o xemit_lamch emit_lamch.o -lm
/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/bin/ATLrun.sh /private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/tune/sysinfo xemit_lamch
cp res/atlas_?lamch.h /private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/include/.
make[3]: Leaving directory '/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/tune/sysinfo'
make[2]: Leaving directory '/private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/bin'
building of '/nix/store/8738r52can3dwx2crgbzxbd6i2whip9r-atlas-3.10.3.drv' timed out after 1800 seconds
cannot build derivation '/nix/store/mjmsqf8v1bn0v4c4mdrwvimdpilnk6a6-liblapack-3.8.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/9yk0gicww0ixxm6l0f4pfmjkqljlpg7w-openblas-liblapack-join.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/riznj4i48pfa7f102ggx8jcv11iksyib-python3.6-cvxopt-1.2.0.drv': 1 dependencies couldn't be built
�[31;1merror:�[0m build of '/nix/store/riznj4i48pfa7f102ggx8jcv11iksyib-python3.6-cvxopt-1.2.0.drv' failed

timokau · 2018-07-09T11:36:41Z

Turns out neither sage nor cvxopt are at fault but openblas. #43234

GrahamcOfBorg added 10.rebuild-darwin: 0 10.rebuild-linux: 1-10 labels Jul 3, 2018

timokau changed the title ~~sage: fix build~~ [WIP] sage: fix build Jul 3, 2018

timokau changed the title ~~[WIP] sage: fix build~~ [WIP] pythonPackages.cvxopt: fix transient test failure Jul 3, 2018

timokau force-pushed the sage-cvxopt-fix branch from 03257c1 to 0a26b9f Compare July 6, 2018 16:54

timokau requested a review from FRidh as a code owner July 6, 2018 16:54

timokau changed the title ~~[WIP] pythonPackages.cvxopt: fix transient test failure~~ pythonPackages.cvxopt: fix transient test failure Jul 6, 2018

GrahamcOfBorg added the 6.topic: python label Jul 6, 2018

pythonPackages.cvxopt: fix transient test error

b9ea36e

See cvxopt/cvxopt#122 for more info.

timokau force-pushed the sage-cvxopt-fix branch from 0a26b9f to b9ea36e Compare July 6, 2018 17:03

timokau changed the title ~~pythonPackages.cvxopt: fix transient test failure~~ [WIP] pythonPackages.cvxopt: fix transient test failure Jul 6, 2018

GrahamcOfBorg added 10.rebuild-darwin: 1-10 and removed 10.rebuild-darwin: 0 labels Jul 6, 2018

timokau closed this Jul 9, 2018

timokau deleted the sage-cvxopt-fix branch July 9, 2018 11:36

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[WIP] pythonPackages.cvxopt: fix transient test failure #42918

[WIP] pythonPackages.cvxopt: fix transient test failure #42918

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edited

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edited

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[WIP] pythonPackages.cvxopt: fix transient test failure #42918

[WIP] pythonPackages.cvxopt: fix transient test failure #42918

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timokau commented Jul 3, 2018 • edited

Motivation for this change

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edited