Stumped on pytest issue

To: tech-pkg <tech-pkg%netbsd.org@localhost>
Subject: Stumped on pytest issue
From: Jason Bacon <jtocino%gmx.com@localhost>
Date: Sat, 23 Dec 2023 08:29:24 -0600

biology/py-macs2 was broken by the upgrade to cython 3.

My preferred solution is to replace it with py-macs3, but this depends
on wip/py-hmmlearn, which is failing "make test" with the following
error.  Hoping someone has a suggestion on how to fix this.

I want to get py-macs3 committed before the branch in order to unbreak
the atac-seq and chip-seq metapackages.

Thanks...

===> Testing for py311-hmmlearn-0.3.0
cd /home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn/work/hmmlearn-0.3.0 &&
/usr/bin/env USETOOLS=no PTHREAD_CFLAGS=\ -pthread\  PTHREAD_LDFLAGS=\
-pthread PTHREAD_LIBS= PTHREADBASE=/usr NPY_BLAS_LIBS=-lblas
NPY_LAPACK_LIBS=-llapack\ -lblas NPY_CBLAS_LIBS=-lcblas\ -lblas
PYTHON=/home/bacon/Pkgsrc/pkg/bin/python3.11 CC=cc CFLAGS=-O2\
-I/home/bacon/Pkgsrc/pkg/include\ -I/usr/include\
-I/home/bacon/Pkgsrc/pkg/include/python3.11
CPPFLAGS=-I/home/bacon/Pkgsrc/pkg/include/netlib\
-I/home/bacon/Pkgsrc/pkg/include\ -I/usr/include\
-I/home/bacon/Pkgsrc/pkg/include/python3.11 CXX=c++ CXXFLAGS=-O2\
-I/home/bacon/Pkgsrc/pkg/include\ -I/usr/include\
-I/home/bacon/Pkgsrc/pkg/include/python3.11 COMPILER_RPATH_FLAG=-Wl,-R
F77=f77 FC=f77 FFLAGS=-O LANG=C LC_ALL=C LC_COLLATE=C LC_CTYPE=C
LC_MESSAGES=C LC_MONETARY=C LC_NUMERIC=C LC_TIME=C LDFLAGS=-Wl,-zrelro\
-L/home/bacon/Pkgsrc/pkg/lib\ -L/usr/lib\ -Wl,-R/usr/lib\
-Wl,-R/home/bacon/Pkgsrc/pkg/lib LINKER_RPATH_FLAG=-R
PATH=/home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn/work/.cwrapper/bin:/home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn/work/.buildlink/bin:/home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn/work/.gcc/bin:/home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn/work/.tools/bin:/home/bacon/Pkgsrc/pkg/bin:/home/bacon/scripts:/home/bacon/Pkgsrc/pkg/bin:/home/bacon/Pkgsrc/pkg/sbin:/usr/pkg/bin:/home/bacon/scripts:/usr/bin:/bin:/usr/pkg/bin:/usr/local/bin:/sbin:/usr/sbin:/usr/local/sbin:/usr/pkg/sbin:/home/bacon/scripts:/home/bacon/Pkgsrc/pkg/bin:/usr/X11R7/bin
PREFIX=/home/bacon/Pkgsrc/pkg MAKELEVEL=0 CONFIG_SITE=
PKG_SYSCONFDIR=/home/bacon/Pkgsrc/pkg/etc
HOME=/home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn/work/.home
CWRAPPERS_CONFIG_DIR=/home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn/work/.cwrapper/config
CPP=cpp LOCALBASE=/home/bacon/Pkgsrc/pkg X11BASE=/usr/X11R7
PKGMANDIR=man PKGINFODIR=info PKGGNUDIR=gnu/ MAKECONF=/dev/null
OBJECT_FMT=ELF USETOOLS=no BSD_INSTALL_PROGRAM=/usr/bin/install\ -c\ -s\
-o\ bacon\ -g\ users\ -m\ 755 BSD_INSTALL_SCRIPT=/usr/bin/install\ -c\
-o\ bacon\ -g\ users\ -m\ 755 BSD_INSTALL_LIB=/usr/bin/install\ -c\ -o\
bacon\ -g\ users\ -m\ 755 BSD_INSTALL_DATA=/usr/bin/install\ -c\ -o\
bacon\ -g\ users\ -m\ 644 BSD_INSTALL_MAN=/usr/bin/install\ -c\ -o\
bacon\ -g\ users\ -m\ 644 BSD_INSTALL=/usr/bin/install
BSD_INSTALL_PROGRAM_DIR=/usr/bin/install\ -d\ -o\ bacon\ -g\ users\ -m\
755 BSD_INSTALL_SCRIPT_DIR=/usr/bin/install\ -d\ -o\ bacon\ -g\ users\
-m\ 755 BSD_INSTALL_LIB_DIR=/usr/bin/install\ -d\ -o\ bacon\ -g\ users\
-m\ 755 BSD_INSTALL_DATA_DIR=/usr/bin/install\ -d\ -o\ bacon\ -g\ users\
-m\ 755 BSD_INSTALL_MAN_DIR=/usr/bin/install\ -d\ -o\ bacon\ -g\ users\
-m\ 755 BSD_INSTALL_GAME=/usr/bin/install\ -c\ -s\ -o\ bacon\ -g\ users\
-m\ 0755 BSD_INSTALL_GAME_DATA=/usr/bin/install\ -c\ -o\ bacon\ -g\
users\ -m\ 0644 BSD_INSTALL_GAME_DIR=/usr/bin/install\ -d\ -o\ bacon\
-g\ users\ -m\ 0755 INSTALL_INFO=
MAKEINFO=/home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn/work/.tools/bin/makeinfo
FLEX= BISON=
ITSTOOL=/home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn/work/.tools/bin/itstool
GDBUS_CODEGEN=/home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn/work/.tools/bin/gdbus-codegen
PKG_CONFIG=/home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn/work/.tools/bin/pkg-config
PKG_CONFIG_LIBDIR=/home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn/work/.buildlink/lib/pkgconfig:/home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn/work/.buildlink/share/pkgconfig
PKG_CONFIG_LOG=/home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn/work/.pkg-config.log
PKG_CONFIG_PATH=
CWRAPPERS_CONFIG_DIR=/home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn/work/.cwrapper/config
pytest-3.11 --capture=no
============================= test session starts
==============================
platform netbsd9 -- Python 3.11.7, pytest-7.4.3, pluggy-1.3.0
rootdir: /home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn/work/hmmlearn-0.3.0
configfile: setup.cfg
collected 0 items / 1 error


==================================== ERRORS
====================================
________________________ ERROR collecting test session
_________________________
../../../../../pkg/lib/python3.11/site-packages/_pytest/config/__init__.py:641:
in _importconftest
    mod = import_path(conftestpath, mode=importmode, root=rootpath)
../../../../../pkg/lib/python3.11/site-packages/_pytest/pathlib.py:567:
in import_path
    importlib.import_module(module_name)
../../../../../pkg/lib/python3.11/importlib/__init__.py:126: in
import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1204: in _gcd_import
    ???
<frozen importlib._bootstrap>:1176: in _find_and_load
    ???
<frozen importlib._bootstrap>:1126: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:241: in _call_with_frames_removed
    ???
<frozen importlib._bootstrap>:1204: in _gcd_import
    ???
<frozen importlib._bootstrap>:1176: in _find_and_load
    ???
<frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:690: in _load_unlocked
    ???
<frozen importlib._bootstrap_external>:940: in exec_module
    ???
<frozen importlib._bootstrap>:241: in _call_with_frames_removed
    ???
lib/hmmlearn/tests/__init__.py:5: in <module>
    from sklearn.datasets import make_spd_matrix
../../../../../pkg/lib/python3.11/site-packages/sklearn/__init__.py:83:
in <module>
    from .base import clone
../../../../../pkg/lib/python3.11/site-packages/sklearn/base.py:19: in
<module>
    from .utils import _IS_32BIT
../../../../../pkg/lib/python3.11/site-packages/sklearn/utils/__init__.py:15:
in <module>
    from scipy.sparse import issparse
../../../../../pkg/lib/python3.11/site-packages/scipy/sparse/__init__.py:287:
in <module>
    from . import csgraph
../../../../../pkg/lib/python3.11/site-packages/scipy/sparse/csgraph/__init__.py:185:
in <module>
    from ._laplacian import laplacian
../../../../../pkg/lib/python3.11/site-packages/scipy/sparse/csgraph/_laplacian.py:7:
in <module>
    from scipy.sparse.linalg import LinearOperator
../../../../../pkg/lib/python3.11/site-packages/scipy/sparse/linalg/__init__.py:121:
in <module>
    from ._dsolve import *
../../../../../pkg/lib/python3.11/site-packages/scipy/sparse/linalg/_dsolve/__init__.py:58:
in <module>
    from .linsolve import *
../../../../../pkg/lib/python3.11/site-packages/scipy/sparse/linalg/_dsolve/linsolve.py:11:
in <module>
    from . import _superlu
E   ImportError:
/home/bacon/Pkgsrc/pkg/lib/python3.11/site-packages/scipy/sparse/linalg/_dsolve/_superlu.so:
Undefined PLT symbol "dnrm2_" (symnum = 2)
=========================== short test summary info
============================
ERROR  - ImportError:
/home/bacon/Pkgsrc/pkg/lib/python3.11/site-packages/scipy/spar...
!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection
!!!!!!!!!!!!!!!!!!!!
=============================== 1 error in 0.84s
===============================
*** Error code 2

Stop.
bmake[1]: stopped in /home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn
*** Error code 1

Stop.
bmake: stopped in /home/bacon/Pkgsrc/pkgsrc/wip/py-hmmlearn
Follow-Ups:
- Re: Stumped on pytest issue
  - From: Dr. Thomas Orgis
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