GH Actions: conda-forge tests broken #32113

mkoeppe · 2021-07-03T17:47:54Z

docker-conda-forge-minimal, docker-conda-forge-standard (https://github.com/sagemath/sage/runs/2967006198?check_suite_focus=true)

  [python3-3.9.5]   LD_LIBRARY_PATH=/sage/local/var/tmp/sage/build/python3-3.9.5/src CC='/opt/conda/bin/x86_64-conda-linux-gnu-cc -pthread' LDSHARED='/opt/conda/bin/x86_64-conda-linux-gnu-cc -pthread -shared -Wl,-rpath-link,/sage/local/lib -L/sage/local/lib -Wl,-rpath,/sage/local/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -L. -Wl,-rpath-link,/sage/local/lib -L/sage/local/lib -Wl,-rpath,/sage/local/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib  ' OPT='-DNDEBUG -g -fwrapv -O3 -Wall' 	_TCLTK_INCLUDES='' _TCLTK_LIBS='' 	./python -E ./setup.py  build
  [python3-3.9.5]   Traceback (most recent call last):
  [python3-3.9.5]     File "/sage/local/var/tmp/sage/build/python3-3.9.5/src/./setup.py", line 33, in <module>
  [python3-3.9.5]       from distutils import log
  [python3-3.9.5]     File "/opt/conda/lib/python3.9/site-packages/_distutils_hack/__init__.py", line 80, in create_module
  [python3-3.9.5]       return importlib.import_module('._distutils', 'setuptools')
  [python3-3.9.5]     File "/opt/conda/lib/python3.9/importlib/__init__.py", line 127, in import_module
  [python3-3.9.5]       return _bootstrap._gcd_import(name[level:], package, level)
  [python3-3.9.5]     File "/opt/conda/lib/python3.9/site-packages/setuptools/__init__.py", line 16, in <module>
  [python3-3.9.5]       from setuptools.extern.six import PY3, string_types
  [python3-3.9.5]     File "/opt/conda/lib/python3.9/site-packages/setuptools/extern/__init__.py", line 50, in load_module
  [python3-3.9.5]       raise ImportError(
  [python3-3.9.5]   ImportError: The 'six' package is required; normally this is bundled with this package so if you get this warning, consult the packager of your distribution.
  [python3-3.9.5]   make[3]: *** [Makefile:641: sharedmods] Error 1

conda-forge-ubuntu (https://github.com/sagemath/sage/runs/2967003736?check_suite_focus=true):

local-conda-forge-ubuntu-minimal run-test: commands[5] | bash -c 'if [ ! -x /home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-minimal/conda/bin/conda ]; then curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname | sed s/^Darwin/MacOSX/;)-x86_64.sh -C - -o /home/runner/work/sage/sage/.tox/Caches/Miniforge3-$(uname | sed s/^Darwin/MacOSX/;)-x86_64.sh && bash /home/runner/work/sage/sage/.tox/Caches/Miniforge3-$(uname | sed s/^Darwin/MacOSX/;)-x86_64.sh -b -f -p /home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-minimal/conda; fi'
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   160  100   160    0     0    935      0 --:--:-- --:--:-- --:--:--   935

100   634  100   634    0     0   1962      0 --:--:-- --:--:-- --:--:--  1962

 22 69.9M   22 15.6M    0     0  15.6M      0  0:00:04 --:--:--  0:00:04 15.6M
 61 69.9M   61 42.8M    0     0  20.8M      0  0:00:03  0:00:02  0:00:01 25.7M
100 69.9M  100 69.9M    0     0  25.0M      0  0:00:02  0:00:02 --:--:-- 30.2M
PREFIX=/home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-minimal/conda
Unpacking payload ...
ERROR   Expected environment not found at prefix: /home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-minimal/conda
ERROR   Aborting.
/home/runner/work/sage/sage/.tox/Caches/Miniforge3-Linux-x86_64.sh: line 365: /home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-minimal/conda/preconda.tar.bz2: No such file or directory

Likewise on local-conda-forge-macos, https://github.com/sagemath/sage/runs/2967003146?check_suite_focus=true

Depends on #30766
Depends on #32894

CC: @isuruf @videlec @dimpase @kliem

Component: porting

Author: Matthias Koeppe

Branch/Commit: f3116a1

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/32113

The text was updated successfully, but these errors were encountered:

isuruf · 2021-07-03T20:57:20Z

comment:1

Can you try removing SETUPTOOLS_USE_DISTUTILS=local for now?

mkoeppe · 2021-07-03T22:40:08Z

comment:2

Sure, we can conditionalize this on CONDA_PREFIX like in build/pkgs/pillow/spkg-install.in

mkoeppe · 2021-09-25T22:35:32Z

Dependencies: #32558, #32557

isuruf · 2021-09-28T21:28:20Z

Branch: u/isuruf/conda

isuruf · 2021-09-28T21:28:20Z

Author: Isuru Fernando

isuruf · 2021-09-28T21:28:20Z

comment:5

Added a branch. Needs to be tested after merging in the dependencies.

isuruf · 2021-09-28T21:28:20Z

Commit: 330db42

sagetrac-git · 2021-09-28T21:29:10Z

Branch pushed to git repo; I updated commit sha1. New commits:

`ec983bd`	`fix for conda python`
`e193a82`	`Need rpath too when building python and override CONFIGURE_LDFLAGS only`
`ccdd330`	`allow building with different compilers on debian/ubuntu`

sagetrac-git · 2021-09-28T21:29:10Z

Changed commit from 330db42 to ccdd330

sagetrac-git · 2021-09-28T21:30:09Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`a95daa0`	`Need rpath too when building python and override CONFIGURE_LDFLAGS only`
`b85cfba`	`allow building with different compilers on debian/ubuntu`

sagetrac-git · 2021-09-28T21:30:09Z

Changed commit from ccdd330 to b85cfba

sagetrac-git · 2021-09-29T16:47:59Z

Branch pushed to git repo; I updated commit sha1. New commits:

`2d4421c`	`update compiling on debian patch`

sagetrac-git · 2021-09-29T16:47:59Z

Changed commit from b85cfba to 2d4421c

sagetrac-git · 2021-09-29T21:13:05Z

Branch pushed to git repo; I updated commit sha1. New commits:

`9a38a29`	`run 2to3 manually for nose`

sagetrac-git · 2021-09-29T21:13:05Z

Changed commit from 2d4421c to 9a38a29

isuruf · 2021-09-29T21:13:27Z

Changed dependencies from #32558, #32557 to #32558, #32557, #32424

isuruf · 2021-09-29T21:13:27Z

New commits:

`9a38a29`	`run 2to3 manually for nose`

dimpase · 2021-09-29T23:16:47Z

comment:12

how about dropping nose? All the packages that used it have swithed to pytests.

isuruf · 2021-09-29T23:17:41Z

comment:13

pytest is optional at the moment. Let's start a vote to drop nose and promote pytest to standard

mkoeppe · 2021-10-13T06:34:23Z

Changed dependencies from #32558, #32557, #32424 to #32558, #32557, #32424, #32595

mkoeppe · 2021-10-13T06:34:23Z

comment:14

The latest run, with 9.3.beta5, of local-conda-forge-macos-standard (https://github.com/sagemath/sage/runs/3863933907?check_suite_focus=true) looks better but uses XCode's python3, as #31539 is still unresolved.

mkoeppe · 2021-10-22T19:11:18Z

Changed branch from u/isuruf/conda to u/mkoeppe/conda

mkoeppe · 2021-10-22T19:11:59Z

comment:16

Not sure if my rebase of the rpath business will work as intended

New commits:

`a579725`	`Need rpath too when building python and override CONFIGURE_LDFLAGS only`
`e458a39`	`allow building with different compilers on debian/ubuntu`
`ee6256d`	`update compiling on debian patch`

mkoeppe · 2021-10-24T06:22:34Z

comment:17

https://github.com/mkoeppe/sage/runs/3986317613?check_suite_focus=true

local-conda-forge-macos-minimal create: /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal
local-conda-forge-macos-minimal run-test-pre: PYTHONHASHSEED='3748675463'
local-conda-forge-macos-minimal run-test: commands[0] | bash -c 'if [ ! -d /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/Library/Caches ]; then mkdir -p /Users/runner/work/sage/sage/.tox/Caches && mkdir -p /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/Library && ln -sf /Users/runner/work/sage/sage/.tox/Caches /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/Library/; fi'
local-conda-forge-macos-minimal run-test: commands[1] | bash -c 'mkdir -p /Users/runner/work/sage/sage/.tox/Caches/conda_pkgs /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/conda'
local-conda-forge-macos-minimal run-test: commands[2] | bash -c 'echo >  /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/conda/.condarc "pkgs_dirs:"'
local-conda-forge-macos-minimal run-test: commands[3] | bash -c 'echo >> /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/conda/.condarc "  - /Users/runner/work/sage/sage/.tox/Caches/conda_pkgs"'
local-conda-forge-macos-minimal run-test: commands[4] | bash -c 'cat condarc.yml >> /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/conda/.condarc'
local-conda-forge-macos-minimal run-test: commands[5] | bash -c 'if [ ! -x /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/conda/bin/conda ]; then mkdir /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/conda/conda-meta && curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname | sed s/^Darwin/MacOSX/;)-x86_64.sh -C - -o /Users/runner/work/sage/sage/.tox/Caches/Miniforge3-$(uname | sed s/^Darwin/MacOSX/;)-x86_64.sh && bash /Users/runner/work/sage/sage/.tox/Caches/Miniforge3-$(uname | sed s/^Darwin/MacOSX/;)-x86_64.sh -b -f -p /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/conda; fi'
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   161  100   161    0     0    800      0 --:--:-- --:--:-- --:--:--   805

100   635  100   635    0     0   1819      0 --:--:-- --:--:-- --:--:--  1819

 13 41.5M   13 5778k    0     0  8161k      0  0:00:05 --:--:--  0:00:05 8161k
100 41.5M  100 41.5M    0     0  31.2M      0  0:00:01  0:00:01 --:--:-- 57.9M
PREFIX=/Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/conda
Unpacking payload ...
ERROR   Configuration file specified but does not exist at 'condarc.yml'
ERROR   Aborting.
/Users/runner/work/sage/sage/.tox/Caches/Miniforge3-MacOSX-x86_64.sh: line 364: /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/conda/preconda.tar.bz2: No such file or directory
ERROR: InvocationError for command /bin/bash -c 'if [ ! -x /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/conda/bin/conda ]; then mkdir /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/conda/conda-meta && curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname | sed s/^Darwin/MacOSX/;)-x86_64.sh -C - -o /Users/runner/work/sage/sage/.tox/Caches/Miniforge3-$(uname | sed s/^Darwin/MacOSX/;)-x86_64.sh && bash /Users/runner/work/sage/sage/.tox/Caches/Miniforge3-$(uname | sed s/^Darwin/MacOSX/;)-x86_64.sh -b -f -p /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/conda; fi' (exited with code 1)

sagetrac-git · 2021-12-20T22:28:32Z

Changed commit from ee6256d to e6b912b

sagetrac-git · 2021-12-20T22:28:32Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`7030a0f`	`Need rpath too when building python and override CONFIGURE_LDFLAGS only`
`5af7789`	`allow building with different compilers on debian/ubuntu`
`e5d336f`	`update compiling on debian patch`
`e6b912b`	`tox.ini: Do not set environment variable CONDARC`

mkoeppe · 2021-12-20T22:29:17Z

Changed dependencies from #32558, #32557, #32424, #32595 to none

mkoeppe · 2021-12-20T22:29:17Z

Changed author from Isuru Fernando to Isuru Fernando, Matthias Koeppe

mkoeppe · 2021-12-20T23:50:06Z

comment:21

The last commit fixes ERROR Configuration file specified but does not exist at 'condarc.yml'

mkoeppe · 2021-12-20T23:51:22Z

comment:22

With tox -e docker-conda-forge-minimal I get:

  [openblas-0.3.18]   /opt/conda/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -O2 -DMAX_STACK_ALLOC=2048 -Wall -m64 -DF_INTERFACE_GFORT -fPIC -DSMP_SERVER -DNO_WARMUP -DMAX_CPU_NUMBER=10 -DMAX_PARALLEL_NUMBER=1 -DUSE_TLS -DBUILD_SINGLE=1 -DBUILD_DOUBLE=1 -DBUILD_COMPLEX=1 -DBUILD_COMPLEX16=1 -DVERSION=\"0.3.18\" -msse3 -mssse3 -UASMNAME -UASMFNAME -UNAME -UCNAME -UCHAR_NAME -UCHAR_CNAME -DASMNAME= -DASMFNAME=_ -DNAME=_ -DCNAME= -DCHAR_NAME=\"_\" -DCHAR_CNAME=\"\" -DNO_AFFINITY -I. -O2 -DSMALL_MATRIX_OPT -DMAX_STACK_ALLOC=2048 -Wall -m64 -DF_INTERFACE_GFORT -fPIC -DSMP_SERVER -DNO_WARMUP -DMAX_CPU_NUMBER=10 -DMAX_PARALLEL_NUMBER=1 -DUSE_TLS -DBUILD_SINGLE=1 -DBUILD_DOUBLE=1 -DBUILD_COMPLEX=1 -DBUILD_COMPLEX16=1 -DVERSION=\"0.3.18\" -msse3 -mssse3 -UASMNAME -UASMFNAME -UNAME -UCNAME -UCHAR_NAME -UCHAR_CNAME -DASMNAME= -DASMFNAME=_ -DNAME=_ -DCNAME= -DCHAR_NAME=\"_\" -DCHAR_CNAME=\"\" -DNO_AFFINITY -I.. -Wl,-rpath-link,/sage/local/lib -L/sage/local/lib -Wl,-rpath,/sage/local/lib -Wl,-rpath-link,/sage/local/lib -L/sage/local/lib -Wl,-rpath,/sage/local/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -w -o linktest linktest.c ../libopenblas_atomp-r0.3.18.so -L/opt/conda/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0 -L/opt/conda/bin/../lib/gcc -L/sage/local/lib/../lib -L/sage/local/lib/../lib -L/opt/conda/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/lib/../lib -L/opt/conda/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../lib -L/opt/conda/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib -L/opt/conda/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib -L/sage/local/lib -L/sage/local/lib -L/opt/conda/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/lib -L/opt/conda/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../.. -L/opt/conda/bin/../x86_64-conda-linux-gnu/sysroot/lib -L/opt/conda/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib -Wl,-rpath,/opt/conda/lib  -lgfortran -lm -lquadmath -lm -lc   && echo OK.
  [openblas-0.3.18]   /opt/conda/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../libopenblas_atomp-r0.3.18.so: undefined reference to `GOMP_parallel'
  [openblas-0.3.18]   /opt/conda/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../libopenblas_atomp-r0.3.18.so: undefined reference to `omp_get_thread_num_'
  [openblas-0.3.18]   /opt/conda/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../libopenblas_atomp-r0.3.18.so: undefined reference to `omp_get_num_threads_'
  [openblas-0.3.18]   /opt/conda/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../libopenblas_atomp-r0.3.18.so: undefined reference to `GOMP_task'
  [openblas-0.3.18]   /opt/conda/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../libopenblas_atomp-r0.3.18.so: undefined reference to `omp_get_thread_num'
  [openblas-0.3.18]   collect2: error: ld returned 1 exit status
  [openblas-0.3.18]   make[4]: *** [Makefile:186: ../libopenblas_atomp-r0.3.18.so] Error 1
  [openblas-0.3.18]   make[4]: Target 'so' not remade because of errors.
  [openblas-0.3.18]   make[3]: *** [Makefile:122: shared] Error 2
  [openblas-0.3.18]   ********************************************************************************
  [openblas-0.3.18]   Error building openblas-0.3.18
  [openblas-0.3.18]   ********************************************************************************

mkoeppe · 2021-12-20T23:52:10Z

comment:23

With tox -e docker-conda-forge-standard I get a build error with primecount. That's now #33054.

mkoeppe · 2021-12-21T01:02:48Z

Dependencies: #30766

sagetrac-git · 2021-12-21T01:03:07Z

Changed commit from e6b912b to c0b5b67

sagetrac-git · 2021-12-21T01:03:07Z

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

`63078ac`	`build/pkgs/terminado: Update to 0.12.1`
`22de5dc`	`build/pkgs/notebook: Update to 6.4.6`
`a0fe18b`	`build/pkgs/nbclient: Update to 0.5.4`
`ef3fc7f`	`build/pkgs/jupyter_client: Update to 7.1.0`
`a593bc9`	`build/pkgs/jupyter_core: Update to 4.9.1`
`66c16b1`	`build/pkgs/importlib_metadata: Update to 4.8.2`
`02aa94c`	`Merge #32930`
`249357d`	`sage.cpython.atexit: fix for python 3.10 (#30766)`
`df9f1d4`	`Pass float(0.5) to time.sleep`
`c0b5b67`	`Merge #30766`

mkoeppe · 2021-12-21T01:35:38Z

Changed dependencies from #30766 to #30766, #32894

mkoeppe · 2021-12-21T03:24:59Z

comment:27

I've put the commits for fixing the python3 spkg build on #33055.

Here on this ticket, I'll focus on getting the conda-forge-standard builds to work (using conda's python) - the python3 patches are not needed here.

sagetrac-git · 2021-12-21T03:26:37Z

Changed commit from c0b5b67 to f3116a1

sagetrac-git · 2021-12-21T03:26:37Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. Last 10 new commits:

`de7de85`	`cython is not in toolchain!`
`43d481b`	`bump to 0.1.0`
`f66821b`	`cysignals are needed`
`ae37b4e`	`deprecate sage.interfaces.primecount, not just remove`
`d3ae5f4`	`primecount is on conda, too`
`3a8c7fe`	`primesieve is on conda, too`
`74b3845`	`allow float inputs for prime_pi`
`591be34`	`Merge #32894`
`049a5f6`	`tox.ini: Do not set environment variable CONDARC`
`f3116a1`	`tox.ini (conda): Force use of conda's python3`

mkoeppe · 2021-12-21T03:27:02Z

Changed author from Isuru Fernando, Matthias Koeppe to Matthias Koeppe

mkoeppe · 2021-12-21T04:42:27Z

Reviewer: https://github.com/mkoeppe/sage/actions/runs/1605145773

dimpase · 2021-12-23T10:41:10Z

comment:32

lgtm

mkoeppe · 2021-12-23T16:25:27Z

comment:33

Thanks!

mkoeppe · 2021-12-23T16:25:27Z

Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/1605145773 to Dima Pasechnik

vbraun · 2022-01-01T00:23:35Z

Changed branch from u/mkoeppe/conda to f3116a1

mkoeppe added this to the sage-9.4 milestone Jul 3, 2021

mkoeppe added c: porting labels Jul 3, 2021

mkoeppe modified the milestones: sage-9.4, sage-9.5 Aug 22, 2021

isuruf added the s: needs review label Sep 28, 2021

mkoeppe added p: critical / 2 and removed p: major / 3 labels Dec 20, 2021

dimpase added s: positive review and removed s: needs review labels Dec 23, 2021

vbraun removed the s: positive review label Jan 1, 2022

vbraun closed this as completed in 039a909 Jan 1, 2022

GH Actions: conda-forge tests broken #32113

GH Actions: conda-forge tests broken #32113

Comments

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