cysignals, cvxopt fail to build in conda #32087

videlec · 2021-06-29T21:29:58Z

Sage sources 9.4.beta3

Depends on #32387

CC: @isuruf

Component: packages: standard

Branch/Commit: u/isuruf/pari-conda @ 3592860

Issue created by migration from https://trac.sagemath.org/ticket/32087

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

videlec · 2021-06-29T21:30:55Z

Attachment: conda-list.txt

Attachment: config.status.gz

videlec · 2021-06-29T21:31:10Z

Attachment: config.log

videlec · 2021-06-29T21:33:56Z

comment:1

Attachment: pynac-0.7.27.p8.log

kiwifb · 2021-06-29T21:37:26Z

comment:3

Any idea where the -nostdlib could have originated in the final link line? I am fairly sure it is why the linker tries to link to static version of the pthread library. It probably also tries to use a static version of libstdc++.

mkoeppe · 2021-06-29T21:39:25Z

comment:4

From the build log:

libtool: link: /home/vincent/miniconda3/envs/sage-build/bin/x86_64-conda-linux-gnu-c++  -fPIC -DPIC -shared -nostdlib /home/vincent/miniconda3/envs/sage-build/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/crti.o /home/vincent/miniconda3/envs/sage-build/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/crtbeginS.o  .libs/libpynac_la-add.o .libs/libpynac_la-archive.o .libs/libpynac_la-assume.o .libs/libpynac_la-basic.o .libs/libpynac_la-cmatcher.o .libs/libpynac_la-constant.o .libs/libpynac_la-context.o .libs/libpynac_la-ex.o .libs/libpynac_la-expair.o .libs/libpynac_la-expairseq.o .libs/libpynac_la-exprseq.o .libs/libpynac_la-fderivative.o .libs/libpynac_la-function.o .libs/libpynac_la-function_info.o .libs/libpynac_la-infinity.o .libs/libpynac_la-inifcns.o .libs/libpynac_la-inifcns_trig.o .libs/libpynac_la-inifcns_zeta.o .libs/libpynac_la-inifcns_hyperb.o .libs/libpynac_la-inifcns_trans.o .libs/libpynac_la-inifcns_gamma.o .libs/libpynac_la-inifcns_nstdsums.o .libs/libpynac_la-inifcns_orthopoly.o .libs/libpynac_la-inifcns_hyperg.o .libs/libpynac_la-inifcns_comb.o .libs/libpynac_la-lst.o .libs/libpynac_la-matrix.o .libs/libpynac_la-mpoly-giac.o .libs/libpynac_la-mpoly-ginac.o .libs/libpynac_la-mpoly-singular.o .libs/libpynac_la-mpoly.o .libs/libpynac_la-mul.o .libs/libpynac_la-normal.o .libs/libpynac_la-numeric.o .libs/libpynac_la-operators.o .libs/libpynac_la-power.o .libs/libpynac_la-py_funcs.o .libs/libpynac_la-registrar.o .libs/libpynac_la-relational.o .libs/libpynac_la-remember.o .libs/libpynac_la-pseries.o .libs/libpynac_la-print.o .libs/libpynac_la-symbol.o .libs/libpynac_la-upoly-ginac.o .libs/libpynac_la-utils.o .libs/libpynac_la-wildcard.o .libs/libpynac_la-templates.o .libs/libpynac_la-infoflagbase.o .libs/libpynac_la-sum.o .libs/libpynac_la-order.o .libs/libpynac_la-useries.o   -L/opt/sage/local/lib -L/home/vincent/miniconda3/envs/sage-build/lib -lpthread -lfactory -lmpfr -lntl -lomalloc -lsingular_resources -lflint -lgmp -L/home/vincent/miniconda3/envs/sage-build/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0 -L/home/vincent/miniconda3/envs/sage-build/bin/../lib/gcc -L/home/vincent/miniconda3/envs/sage-build/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/lib/../lib -L/home/vincent/miniconda3/envs/sage-build/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib -L/home/vincent/miniconda3/envs/sage-build/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib -L/home/vincent/miniconda3/envs/sage-build/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/lib -L/home/vincent/miniconda3/envs/sage-build/bin/../x86_64-conda-linux-gnu/sysroot/lib -L/home/vincent/miniconda3/envs/sage-build/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib -lstdc++ -lm -lc -lgcc_s /home/vincent/miniconda3/envs/sage-build/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/crtendS.o /home/vincent/miniconda3/envs/sage-build/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/crtn.o  -O2 -g -march=nocona -mtune=haswell -fstack-protector-strong -O2 -Wl,-rpath-link -Wl,/opt/sage/local/lib -Wl,-rpath -Wl,/opt/sage/local/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath -Wl,/home/vincent/miniconda3/envs/sage-build/lib -Wl,-rpath-link -Wl,/home/vincent/miniconda3/envs/sage-build/lib -pthread -Wl,--sysroot=/ -Wl,-rpath -Wl,/home/vincent/miniconda3/envs/sage-build/lib -Wl,-rpath-link -Wl,/home/vincent/miniconda3/envs/sage-build/lib -Wl,-rpath -Wl,/home/vincent/miniconda3/envs/sage-build/lib -Wl,-rpath-link -Wl,/home/vincent/miniconda3/envs/sage-build/lib -Wl,-rpath-link -Wl,/opt/sage/local/lib -Wl,-rpath -Wl,/opt/sage/local/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath -Wl,/home/vincent/miniconda3/envs/sage-build/lib -Wl,-rpath-link -Wl,/home/vincent/miniconda3/envs/sage-build/lib -march=nocona -mtune=haswell -fstack-protector-strong -O2 -O2   -pthread -Wl,-soname -Wl,libpynac.so.18 -o .libs/libpynac.so.18.3.5
1163	/home/vincent/miniconda3/envs/sage-build/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find /usr/lib64/libpthread_nonshared.a
1164

mkoeppe · 2021-06-29T21:40:28Z

comment:5

pynac gets its flags from python, see https://github.com/pynac/pynac/blob/master/configure.ac#L56

videlec · 2021-06-29T21:45:09Z

comment:6

Note that for this build I explicitely used conda's Python with

$ ./configure --with-python=/home/vincent/miniconda3/envs/sage-build/bin/python3

kiwifb · 2021-06-29T21:48:00Z

comment:7

A good question for @isuruf then. -nostdlib is usually used to link C++ code completely statically. It should only be used in conjunction with static. If you try to link C++ statically without -nostdlib various standard library will still be dynamically linked. It is a nuclear option to get statically linked C++ code.

Not recommended for use unless you really know what you are doing or you are compiling for a BlueGene [now completely dead, I personally shutdown two of those in 2016].

isuruf · 2021-06-29T22:12:35Z

comment:8

-nostdlib is added by libtool. This is a different problem. Can you send the output of conda list -p /home/vincent/miniconda3/envs/sage-build/ and also what the value of _CONDA_PYTHON_SYSCONFIGDATA_NAME and PYTHON_SYSCONFIGDATA_NAME in your env is?

videlec · 2021-06-30T06:50:41Z

comment:9

Got

$ echo $_CONDA_PYTHON_SYSCONFIGDATA_NAME
_sysconfigdata_x86_64_conda_cos6_linux_gnu
$ echo $PYTHON_SYSCONFIGDATA_NAME

And the output of conda list -p /home/vincent/miniconda3/envs/sage-build/ is in conda-list-p.txt.

isuruf · 2021-06-30T14:17:53Z

comment:10

Attachment: conda-list-p.txt

Thanks. Can you post the output of python -m sysconfig | grep sysroot?

videlec · 2021-06-30T14:55:51Z

comment:11

	CONFIG_ARGS = "'--prefix=/home/vincent/miniconda3/envs/sage-build' '--build=x86_64-conda_cos6-linux-gnu' '--host=x86_64-conda_cos6-linux-gnu' '--enable-ipv6' '--with-ensurepip=no' '--with-tzpath=/home/vincent/miniconda3/envs/sage-build/share/zoneinfo:/home/vincent/miniconda3/envs/sage-build/share/tzinfo' '--with-computed-gotos' '--with-system-ffi' '--enable-loadable-sqlite-extensions' '--with-tcltk-includes=-I/home/vincent/miniconda3/envs/sage-build/include' '--with-tcltk-libs=-L/home/vincent/miniconda3/envs/sage-build/lib -ltcl8.6 -ltk8.6' '--with-platlibdir=lib' '--with-lto' '--enable-optimizations' '-oldincludedir=/home/conda/feedstock_root/build_artifacts/python-split_1624061905143/_build_env/x86_64-conda_cos6-linux-gnu/sysroot/usr/include' '--disable-shared' 'PROFILE_TASK=-m test --pgo' 'build_alias=x86_64-conda_cos6-linux-gnu' 'host_alias=x86_64-conda_cos6-linux-gnu' 'MACHDEP=linux' 'CC=x86_64-conda_cos6-linux-gnu-gcc' 'CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/vincent/miniconda3/envs/sage-build/include      ' 'LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/vincent/miniconda3/envs/sage-build/lib -Wl,-rpath-link,/home/vincent/miniconda3/envs/sage-build/lib -L/home/vincent/miniconda3/envs/sage-build/lib' 'CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/vincent/miniconda3/envs/sage-build/include -I/home/vincent/miniconda3/envs/sage-build/include' 'CPP=/home/conda/feedstock_root/build_artifacts/python-split_1624061905143/_build_env/bin/x86_64-conda_cos6-linux-gnu-cpp' 'PKG_CONFIG_PATH=/home/vincent/miniconda3/envs/sage-build/lib/pkgconfig'"

isuruf · 2021-06-30T23:20:28Z

comment:12

Sorry, I can't reproduce this. All I know is that the flag -Wl,--sysroot=/ is the issue here. This is used in a sysconfig when used with compilers other than the ones shipped with conda. (It's there to use our newer linker with an older gcc installation). This shouldn't happen when conda compilers are used where _CONDA_PYTHON_SYSCONFIGDATA_NAME is set. The only situation I can think of is sage or pynac stripping the environment and deleting that env variable.

Can you try printing that env variable _CONDA_PYTHON_SYSCONFIGDATA_NAME at the beginning of pynac build to confirm that sage doesn't filter it out?

isuruf · 2021-07-01T00:26:00Z

comment:13

Nvm, I can reproduce this. I'll fix this soon.

isuruf · 2021-07-01T04:06:05Z

comment:14

Upstream issue conda-forge/python-feedstock#474.

You can downgrade your setuptools version as a workaround.

videlec · 2021-07-01T15:53:48Z

comment:15

Replying to @isuruf:

Upstream issue conda-forge/python-feedstock#474.

You can downgrade your setuptools version as a workaround.

Downgrading to setuptools 49.5.0 was only possible together with downgrading Python to 3.8. I am trying to build sage with that new setup now.

videlec · 2021-07-02T06:39:42Z

comment:16

Same problem

libtool: link: /home/vincent/miniconda3/envs/sage-build/bin/x86_64-conda-linux-gnu-c++  -fPIC -DPIC -shared -nostdlib /home/vincent/miniconda3/envs/sage-build/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/crti.o /home/vincent/miniconda3/envs/sage-build/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/crtbeginS.o  .libs/libpynac_la-add.o .libs/libpynac_la-archive.o .libs/libpynac_la-assume.o .libs/libpynac_la-basic.o .libs/libpynac_la-cmatcher.o .libs/libpynac_la-constant.o .libs/libpynac_la-context.o .libs/libpynac_la-ex.o .libs/libpynac_la-expair.o .libs/libpynac_la-expairseq.o .libs/libpynac_la-exprseq.o .libs/libpynac_la-fderivative.o .libs/libpynac_la-function.o .libs/libpynac_la-function_info.o .libs/libpynac_la-infinity.o .libs/libpynac_la-inifcns.o .libs/libpynac_la-inifcns_trig.o .libs/libpynac_la-inifcns_zeta.o .libs/libpynac_la-inifcns_hyperb.o .libs/libpynac_la-inifcns_trans.o .libs/libpynac_la-inifcns_gamma.o .libs/libpynac_la-inifcns_nstdsums.o .libs/libpynac_la-inifcns_orthopoly.o .libs/libpynac_la-inifcns_hyperg.o .libs/libpynac_la-inifcns_comb.o .libs/libpynac_la-lst.o .libs/libpynac_la-matrix.o .libs/libpynac_la-mpoly-giac.o .libs/libpynac_la-mpoly-ginac.o .libs/libpynac_la-mpoly-singular.o .libs/libpynac_la-mpoly.o .libs/libpynac_la-mul.o .libs/libpynac_la-normal.o .libs/libpynac_la-numeric.o .libs/libpynac_la-operators.o .libs/libpynac_la-power.o .libs/libpynac_la-py_funcs.o .libs/libpynac_la-registrar.o .libs/libpynac_la-relational.o .libs/libpynac_la-remember.o .libs/libpynac_la-pseries.o .libs/libpynac_la-print.o .libs/libpynac_la-symbol.o .libs/libpynac_la-upoly-ginac.o .libs/libpynac_la-utils.o .libs/libpynac_la-wildcard.o .libs/libpynac_la-templates.o .libs/libpynac_la-infoflagbase.o .libs/libpynac_la-sum.o .libs/libpynac_la-order.o .libs/libpynac_la-useries.o   -L/opt/sage/local/lib -L/home/vincent/miniconda3/envs/sage-build/lib -lpthread -lfactory -lmpfr -lntl -lomalloc -lsingular_resources -lflint -lgmp -L/home/vincent/miniconda3/envs/sage-build/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0 -L/home/vincent/miniconda3/envs/sage-build/bin/../lib/gcc -L/home/vincent/miniconda3/envs/sage-build/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/lib/../lib -L/home/vincent/miniconda3/envs/sage-build/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib -L/home/vincent/miniconda3/envs/sage-build/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib -L/home/vincent/miniconda3/envs/sage-build/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/lib -L/home/vincent/miniconda3/envs/sage-build/bin/../x86_64-conda-linux-gnu/sysroot/lib -L/home/vincent/miniconda3/envs/sage-build/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib -lstdc++ -lm -lc -lgcc_s /home/vincent/miniconda3/envs/sage-build/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/crtendS.o /home/vincent/miniconda3/envs/sage-build/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/crtn.o  -O2 -g -march=nocona -mtune=haswell -fstack-protector-strong -O2 -Wl,-rpath-link -Wl,/opt/sage/local/lib -Wl,-rpath -Wl,/opt/sage/local/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath -Wl,/home/vincent/miniconda3/envs/sage-build/lib -Wl,-rpath-link -Wl,/home/vincent/miniconda3/envs/sage-build/lib -pthread -Wl,-rpath=/home/vincent/miniconda3/envs/sage-build/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,-rpath-link -Wl,/opt/sage/local/lib -Wl,-rpath -Wl,/opt/sage/local/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath -Wl,/home/vincent/miniconda3/envs/sage-build/lib -Wl,-rpath-link -Wl,/home/vincent/miniconda3/envs/sage-build/lib -march=nocona -mtune=haswell -fstack-protector-strong -O2 -O2   -pthread -Wl,-soname -Wl,libpynac.so.18 -o .libs/libpynac.so.18.3.5
/home/vincent/miniconda3/envs/sage-build/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find /usr/lib64/libpthread_nonshared.a
collect2: error: ld returned 1 exit status

Note that sage installs its own version of setuptools (version 56.2.0).

isuruf · 2021-07-02T06:46:26Z

comment:17

Right. Until upstream issue is solved, we have to downgrade setuptools to 49.* in sage itself.

mkoeppe · 2021-07-02T06:58:28Z

comment:18

Perhaps it's good enough to just change the value of SETUPTOOLS_USE_DISTUTILS (set in build/bin/sage-build-env) for conda as a workaround?

isuruf · 2021-07-02T21:33:16Z

comment:19

Yes, that seems reasonable until we get the upstream issue solved.

videlec · 2021-07-06T20:25:02Z

comment:20

Replying to @mkoeppe:

Perhaps it's good enough to just change the value of SETUPTOOLS_USE_DISTUTILS (set in build/bin/sage-build-env) for conda as a workaround?

How could I do that?

mkoeppe · 2021-07-06T21:03:28Z

Branch: u/mkoeppe/pynac_fails_to_build_in_conda

mkoeppe · 2021-07-06T21:03:33Z

comment:22

Try this

New commits:

`5ce41d9`	`build/bin/sage-build-env [conda]: Use SETUPTOOLS_USE_DISTUTILS=stdlib`

mkoeppe · 2021-07-06T21:03:33Z

Commit: 5ce41d9

videlec · 2021-07-06T21:37:08Z

comment:23

Successfully installed pynac-0.7.27.p8

Thanks

isuruf · 2021-07-06T22:24:55Z

comment:25

Can you attach the pari log as well?

videlec · 2021-07-06T22:43:44Z

comment:26

Attachment: pari-2.13.1.log

available as pari-2.13.1.log.

Thanks for your help.

mkoeppe · 2021-07-06T22:45:14Z

comment:27

This may be a good moment to mention sagemath/cysignals#125, which needs help

isuruf · 2021-07-09T20:30:27Z

Changed branch from u/mkoeppe/pynac_fails_to_build_in_conda to u/isuruf/pari-conda

isuruf · 2021-07-09T20:30:27Z

New commits:

`e15d3c3`	`remove pari_jupyter conda.txt because it is not compatible with pari=2.13`
`1ea51b6`	`make sure pari>=2.13 is used with conda`
`a2da866`	`set SUITESPARSE_INC_DIR to SAGE_LOCAL/include if we are using system suitesparse`
`27ced51`	`Fix lib dirs for cvxopts`
`3592860`	`Ask for pthread version of pari`

isuruf · 2021-07-09T20:30:27Z

Changed commit from 5ce41d9 to 3592860

isuruf · 2021-07-09T20:31:51Z

comment:29

The issue was what @mkoeppe said about LDFLAGS in python overriding sage built version. For now, I've updated conda in pari to use pthread version for pari>=2.13.

Can you check that this works?

mkoeppe · 2021-07-12T06:59:54Z

comment:32

It looks like this may be breaking cvxopt on a number of platforms - see https://github.com/mkoeppe/sage/runs/3041608561?check_suite_focus=true

videlec · 2021-07-15T09:46:44Z

comment:33

@isuruf: with your branch, sage did build in conda. Thanks. Though I got into trouble when compiling the documentation

[dochtml] Error in sys.excepthook:
[dochtml] Traceback (most recent call last):
[dochtml]   File "/home/vincent/miniconda3/envs/sage-build/lib/python3.9/traceback.py", line 493, in __init__
[dochtml]     context = TracebackException(
[dochtml]   File "/home/vincent/miniconda3/envs/sage-build/lib/python3.9/traceback.py", line 493, in __init__
[dochtml]     context = TracebackException(
[dochtml]   File "/home/vincent/miniconda3/envs/sage-build/lib/python3.9/traceback.py", line 493, in __init__
[dochtml]     context = TracebackException(
[dochtml]   [Previous line repeated 997 more times]
[dochtml] RecursionError: maximum recursion depth exceeded
[dochtml] 
[dochtml] Original exception was:
[dochtml] Traceback (most recent call last):
[dochtml]   File "sage/libs/giac/giac.pyx", line 1121, in sage.libs.giac.giac.Pygen.eval (build/cythonized/sage/libs/giac/giac.cpp:143061)
[dochtml]   File "sage/libs/giac/giac.pyx", line 739, in sage.libs.giac.giac.GiacSetting.eval_level.__get__ (build/cythonized/sage/libs/giac/giac.cpp:10510)
[dochtml]   File "sage/libs/giac/giac.pyx", line 1323, in sage.libs.giac.giac.Pygen.cas_setup (build/cythonized/sage/libs/giac/giac.cpp:145936)
[dochtml]   File "sage/libs/giac/giac.pyx", line 902, in sage.libs.giac.giac.Pygen.__cinit__ (build/cythonized/sage/libs/giac/giac.cpp:140970)
[dochtml] RecursionError: maximum recursion depth exceeded while calling a Python object
[dochtml] 
[dochtml] During handling of the above exception, another exception occurred:
[dochtml] 
[dochtml] Traceback (most recent call last):
[dochtml]   File "sage/libs/giac/giac.pyx", line 1121, in sage.libs.giac.giac.Pygen.eval (build/cythonized/sage/libs/giac/giac.cpp:143061)
[dochtml]   File "sage/libs/giac/giac.pyx", line 739, in sage.libs.giac.giac.GiacSetting.eval_level.__get__ (build/cythonized/sage/libs/giac/giac.cpp:10513)
[dochtml]   File "sage/libs/giac/giac.pyx", line 1036, in sage.libs.giac.giac.Pygen.__getitem__ (build/cythonized/sage/libs/giac/giac.cpp:142492)
[dochtml]   File "sage/libs/giac/giac.pyx", line 1125, in sage.libs.giac.giac.Pygen.eval (build/cythonized/sage/libs/giac/giac.cpp:143137)
[dochtml] RuntimeError
...
[dochtml] During handling of the above exception, another exception occurred:
[dochtml] 
[dochtml] Traceback (most recent call last):
[dochtml]   File "sage/libs/giac/giac.pyx", line 1121, in sage.libs.giac.giac.Pygen.eval (build/cythonized/sage/libs/giac/giac.cpp:143061)
[dochtml]   File "sage/libs/giac/giac.pyx", line 739, in sage.libs.giac.giac.GiacSetting.eval_level.__get__ (build/cythonized/sage/libs/giac/giac.cpp:10513)
[dochtml]   File "sage/libs/giac/giac.pyx", line 1036, in sage.libs.giac.giac.Pygen.__getitem__ (build/cythonized/sage/libs/giac/giac.cpp:142492)
[dochtml]   File "sage/libs/giac/giac.pyx", line 1125, in sage.libs.giac.giac.Pygen.eval (build/cythonized/sage/libs/giac/giac.cpp:143137)
[dochtml] RuntimeError
[dochtml] 
[dochtml] During handling of the above exception, another exception occurred:
[dochtml] 
[dochtml] Traceback (most recent call last):
[dochtml]   File "/home/vincent/miniconda3/envs/sage-build/lib/python3.9/runpy.py", line 197, in _run_module_as_main
[dochtml]     return _run_code(code, main_globals, None,
[dochtml]   File "/home/vincent/miniconda3/envs/sage-build/lib/python3.9/runpy.py", line 87, in _run_code
[dochtml]     exec(code, run_globals)
[dochtml]   File "/opt/sage/local/lib/python3.9/site-packages/sage_docbuild/__main__.py", line 2, in <module>
[dochtml]     main()
[dochtml]   File "/opt/sage/local/lib/python3.9/site-packages/sage_docbuild/__init__.py", line 1813, in main
[dochtml]     builder()
[dochtml]   File "/opt/sage/local/lib/python3.9/site-packages/sage_docbuild/__init__.py", line 809, in _wrapper
[dochtml]     self.write_auto_rest_file(module_name)
[dochtml]   File "/opt/sage/local/lib/python3.9/site-packages/sage_docbuild/__init__.py", line 1104, in write_auto_rest_file
[dochtml]     title = self.get_module_docstring_title(module_name)
[dochtml]   File "/opt/sage/local/lib/python3.9/site-packages/sage_docbuild/__init__.py", line 1065, in get_module_docstring_title
[dochtml]     __import__(module_name)
[dochtml]   File "/opt/sage/local/lib/python3.9/site-packages/sage/libs/giac/__init__.py", line 35, in <module>
[dochtml]     from .giac import giacsettings, libgiac
[dochtml]   File "sage/libs/giac/giac.pyx", line 2261, in init sage.libs.giac.giac (build/cythonized/sage/libs/giac/giac.cpp:168106)
[dochtml]   File "sage/libs/giac/giac.pyx", line 802, in sage.libs.giac.giac.GiacSetting.threads.__set__ (build/cythonized/sage/libs/giac/giac.cpp:11533)
[dochtml]   File "sage/libs/giac/giac.pyx", line 1125, in sage.libs.giac.giac.Pygen.eval (build/cythonized/sage/libs/giac/giac.cpp:143137)
[dochtml] RuntimeError
[dochtml] make[5]: *** [Makefile:20: doc-inventory--reference-libs] Error 1
[dochtml] make[5]: *** Waiting for unfinished jobs....

mkoeppe · 2021-09-25T22:37:49Z

comment:37

pynac issue will disappear with package removal in #32387

mkoeppe · 2021-09-25T22:37:49Z

Dependencies: #32387

mkoeppe · 2021-12-21T05:02:40Z

comment:38

Outdated; in 9.5.beta8 (with #32113), the packages build OK.

mkoeppe · 2021-12-21T05:06:51Z

comment:39

Replying to @videlec:

@isuruf: with your branch, sage did build in conda. Thanks. Though I got into trouble when compiling the documentation

[dochtml] Error in sys.excepthook:
[dochtml] Traceback (most recent call last):
[dochtml]   File "/home/vincent/miniconda3/envs/sage-build/lib/python3.9/traceback.py", line 493, in __init__
[dochtml]     context = TracebackException(
[dochtml]   File "/home/vincent/miniconda3/envs/sage-build/lib/python3.9/traceback.py", line 493, in __init__
[dochtml]     context = TracebackException(
[dochtml]   File "/home/vincent/miniconda3/envs/sage-build/lib/python3.9/traceback.py", line 493, in __init__
[dochtml]     context = TracebackException(
[dochtml]   [Previous line repeated 997 more times]
[dochtml] RecursionError: maximum recursion depth exceeded
[dochtml] 
[dochtml] Original exception was:
[dochtml] Traceback (most recent call last):
[dochtml]   File "sage/libs/giac/giac.pyx", line 1121, in sage.libs.giac.giac.Pygen.eval (build/cythonized/sage/libs/giac/giac.cpp:143061)
[dochtml]   File "sage/libs/giac/giac.pyx", line 739, in sage.libs.giac.giac.GiacSetting.eval_level.__get__ (build/cythonized/sage/libs/giac/giac.cpp:10510)
[dochtml]   File "sage/libs/giac/giac.pyx", line 1323, in sage.libs.giac.giac.Pygen.cas_setup (build/cythonized/sage/libs/giac/giac.cpp:145936)
[dochtml]   File "sage/libs/giac/giac.pyx", line 902, in sage.libs.giac.giac.Pygen.__cinit__ (build/cythonized/sage/libs/giac/giac.cpp:140970)
[dochtml] RecursionError: maximum recursion depth exceeded while calling a Python object
[dochtml] 
[dochtml] During handling of the above exception, another exception occurred:
[dochtml] 
[dochtml] Traceback (most recent call last):
[dochtml]   File "sage/libs/giac/giac.pyx", line 1121, in sage.libs.giac.giac.Pygen.eval (build/cythonized/sage/libs/giac/giac.cpp:143061)
[dochtml]   File "sage/libs/giac/giac.pyx", line 739, in sage.libs.giac.giac.GiacSetting.eval_level.__get__ (build/cythonized/sage/libs/giac/giac.cpp:10513)
[dochtml]   File "sage/libs/giac/giac.pyx", line 1036, in sage.libs.giac.giac.Pygen.__getitem__ (build/cythonized/sage/libs/giac/giac.cpp:142492)
[dochtml]   File "sage/libs/giac/giac.pyx", line 1125, in sage.libs.giac.giac.Pygen.eval (build/cythonized/sage/libs/giac/giac.cpp:143137)
[dochtml] RuntimeError
...

}}}

I've opened #33056 for this.

videlec added this to the sage-9.4 milestone Jun 29, 2021

videlec added c: packages: standard labels Jun 29, 2021

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isuruf added the s: needs review label Jul 9, 2021

mkoeppe changed the title ~~pynac fails to build in conda~~ pynac, cysignals fail to build in conda Jul 9, 2021

isuruf changed the title ~~pynac, cysignals fail to build in conda~~ pynac, cysignals, cvxopt fail to build in conda Jul 9, 2021

mkoeppe added s: needs work and removed s: needs review labels Jul 15, 2021

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

mkoeppe changed the title ~~pynac, cysignals, cvxopt fail to build in conda~~ cysignals, cvxopt fail to build in conda Sep 25, 2021

mkoeppe removed this from the sage-9.5 milestone Dec 21, 2021

mkoeppe added s: needs review and removed s: needs work labels Dec 21, 2021

isuruf added s: positive review and removed s: needs review labels Feb 16, 2022

vbraun removed the s: positive review label Feb 17, 2022

vbraun closed this as completed Feb 17, 2022

cysignals, cvxopt fail to build in conda #32087

cysignals, cvxopt fail to build in conda #32087

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