[Debian-med-packaging] Bug#1064732: nipype: FTBFS: make[1]: *** [debian/rules:39: override_dh_auto_test] Error 1
Lucas Nussbaum
lucas at debian.org
Sun Feb 25 19:38:07 GMT 2024
Source: nipype
Version: 1.8.6-3
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20240224 ftbfs-trixie
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> export PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_nipype/build; \
> cd build && \
> MPLCONFIGDIR=/<<PKGBUILDDIR>>/build LC_ALL=C.UTF-8 py.test-3 -v --doctest-modules -k "not nipype.interfaces.io.BIDSDataGrabber" ../nipype
> ============================= test session starts ==============================
> platform linux -- Python 3.11.8, pytest-7.4.4, pluggy-1.4.0 -- /usr/bin/python3
> cachedir: .pytest_cache
> rootdir: /<<PKGBUILDDIR>>/nipype
> configfile: pytest.ini
> plugins: xdist-3.4.0
> collecting ... collected 2974 items / 1 deselected / 2973 selected
>
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> ../nipype/pipeline/engine/tests/test_nodes.py::test_mapnode_iterfield_type[x_inp2-f_exp2] PASSED [ 93%]
> ../nipype/pipeline/engine/tests/test_nodes.py::test_mapnode_iterfield_type[x_inp3-f_exp3] PASSED [ 93%]
> ../nipype/pipeline/engine/tests/test_nodes.py::test_mapnode_iterfield_type[Str-f_exp4] PASSED [ 93%]
> ../nipype/pipeline/engine/tests/test_nodes.py::test_mapnode_iterfield_type[x_inp5-f_exp5] PASSED [ 93%]
> ../nipype/pipeline/engine/tests/test_nodes.py::test_mapnode_nested PASSED [ 93%]
> ../nipype/pipeline/engine/tests/test_nodes.py::test_mapnode_expansion PASSED [ 93%]
> ../nipype/pipeline/engine/tests/test_nodes.py::test_node_hash PASSED [ 93%]
> ../nipype/pipeline/engine/tests/test_nodes.py::test_outputs_removal PASSED [ 93%]
> ../nipype/pipeline/engine/tests/test_nodes.py::test_inputs_removal PASSED [ 93%]
> ../nipype/pipeline/engine/tests/test_nodes.py::test_outputmultipath_collapse PASSED [ 93%]
> ../nipype/pipeline/engine/tests/test_nodes.py::test_mapnode_single PASSED [ 93%]
> ../nipype/pipeline/engine/tests/test_nodes.py::test_NodeExecutionError PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_utils.py::test_identitynode_removal PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_utils.py::test_clean_working_directory PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_utils.py::test_multi_disconnected_iterable PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_utils.py::test_provenance PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_utils.py::test_mapnode_crash PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_utils.py::test_mapnode_crash2 PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_utils.py::test_mapnode_crash3 PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_utils.py::test_modify_paths_bug PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_utils.py::test_save_load_resultfile[True] PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_utils.py::test_save_load_resultfile[False] PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_utils.py::test_format_node PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_workflows.py::test_init PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_workflows.py::test_connect PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_workflows.py::test_add_nodes PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_workflows.py::test_disconnect PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_workflows.py::test_workflow_add PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_workflows.py::test_doubleconnect PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_workflows.py::test_nested_workflow_doubleconnect PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_workflows.py::test_duplicate_node_check PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_workflows.py::test_outputs_removal_wf[Linear-False-True] PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_workflows.py::test_outputs_removal_wf[Linear-False-False] PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_workflows.py::test_outputs_removal_wf[Linear-True-True] PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_workflows.py::test_outputs_removal_wf[Linear-True-False] PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_workflows.py::test_outputs_removal_wf[MultiProc-False-True] PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_workflows.py::test_outputs_removal_wf[MultiProc-False-False] PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_workflows.py::test_outputs_removal_wf[MultiProc-True-True] PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_workflows.py::test_outputs_removal_wf[MultiProc-True-False] PASSED [ 94%]
> ../nipype/pipeline/engine/tests/test_workflows.py::test_config_setting PASSED [ 94%]
> ../nipype/pipeline/plugins/sge.py::nipype.pipeline.plugins.sge.qsub_sanitize_job_name PASSED [ 94%]
> ../nipype/pipeline/plugins/tests/test_base.py::test_scipy_sparse PASSED [ 95%]
> ../nipype/pipeline/plugins/tests/test_callback.py::test_callback_normal[Linear] PASSED [ 95%]
> ../nipype/pipeline/plugins/tests/test_callback.py::test_callback_normal[MultiProc] PASSED [ 95%]
> ../nipype/pipeline/plugins/tests/test_callback.py::test_callback_normal[LegacyMultiProc] PASSED [ 95%]
> ../nipype/pipeline/plugins/tests/test_callback.py::test_callback_exception[False-Linear] PASSED [ 95%]
> ../nipype/pipeline/plugins/tests/test_callback.py::test_callback_exception[False-MultiProc] PASSED [ 95%]
> ../nipype/pipeline/plugins/tests/test_callback.py::test_callback_exception[False-LegacyMultiProc] PASSED [ 95%]
> ../nipype/pipeline/plugins/tests/test_callback.py::test_callback_exception[True-Linear] PASSED [ 95%]
> ../nipype/pipeline/plugins/tests/test_callback.py::test_callback_exception[True-MultiProc] PASSED [ 95%]
> ../nipype/pipeline/plugins/tests/test_callback.py::test_callback_exception[True-LegacyMultiProc] PASSED [ 95%]
> ../nipype/pipeline/plugins/tests/test_debug.py::test_debug PASSED [ 95%]
> ../nipype/pipeline/plugins/tests/test_legacymultiproc_nondaemon.py::test_run_multiproc_nondaemon_false SKIPPED [ 95%]
> ../nipype/pipeline/plugins/tests/test_legacymultiproc_nondaemon.py::test_run_multiproc_nondaemon_true SKIPPED [ 95%]
> ../nipype/pipeline/plugins/tests/test_linear.py::test_run_in_series PASSED [ 95%]
> ../nipype/pipeline/plugins/tests/test_multiproc.py::test_run_multiproc SKIPPED [ 95%]
> ../nipype/pipeline/plugins/tests/test_multiproc.py::test_no_more_memory_than_specified PASSED [ 95%]
> ../nipype/pipeline/plugins/tests/test_multiproc.py::test_no_more_threads_than_specified PASSED [ 95%]
> ../nipype/pipeline/plugins/tests/test_multiproc.py::test_hold_job_until_procs_available SKIPPED [ 95%]
> ../nipype/pipeline/plugins/tests/test_oar.py::test_run_oargraph SKIPPED [ 95%]
> ../nipype/pipeline/plugins/tests/test_pbs.py::test_run_pbsgraph SKIPPED [ 95%]
> ../nipype/pipeline/plugins/tests/test_sgelike.py::test_crashfile_creation PASSED [ 95%]
> ../nipype/pipeline/plugins/tests/test_somaflow.py::test_run_somaflow SKIPPED [ 95%]
> ../nipype/pipeline/plugins/tests/test_tools.py::test_report_crash PASSED [ 95%]
> ../nipype/testing/decorators.py::nipype.testing.decorators.make_label_dec PASSED [ 95%]
> ../nipype/testing/tests/test_utils.py::test_tempfatfs SKIPPED (Canno...) [ 95%]
> ../nipype/testing/tests/test_utils.py::test_tempfatfs_calledprocesserror PASSED [ 95%]
> ../nipype/testing/tests/test_utils.py::test_tempfatfs_oserror PASSED [ 95%]
> ../nipype/tests/test_nipype.py::test_nipype_info PASSED [ 95%]
> ../nipype/tests/test_nipype.py::test_git_hash SKIPPED (not able to g...) [ 95%]
> ../nipype/tests/test_nipype.py::test_no_et_bare PASSED [ 95%]
> ../nipype/tests/test_nipype.py::test_no_et_multiproc[True-MultiProc] PASSED [ 96%]
> ../nipype/tests/test_nipype.py::test_no_et_multiproc[True-LegacyMultiProc] PASSED [ 96%]
> ../nipype/tests/test_nipype.py::test_no_et_multiproc[False-MultiProc] PASSED [ 96%]
> ../nipype/tests/test_nipype.py::test_no_et_multiproc[False-LegacyMultiProc] PASSED [ 96%]
> ../nipype/utils/docparse.py::nipype.utils.docparse.insert_doc PASSED [ 96%]
> ../nipype/utils/filemanip.py::nipype.utils.filemanip.fname_presuffix PASSED [ 96%]
> ../nipype/utils/filemanip.py::nipype.utils.filemanip.hash_infile PASSED [ 96%]
> ../nipype/utils/filemanip.py::nipype.utils.filemanip.read_stream PASSED [ 96%]
> ../nipype/utils/filemanip.py::nipype.utils.filemanip.split_filename PASSED [ 96%]
> ../nipype/utils/matlabtools.py::nipype.utils.matlabtools.mlab_tempfile PASSED [ 96%]
> ../nipype/utils/misc.py::nipype.utils.misc.str2bool PASSED [ 96%]
> ../nipype/utils/onetime.py::nipype.utils.onetime.setattr_on_read PASSED [ 96%]
> ../nipype/utils/tests/test_cmd.py::TestNipypeCMD::test_main_returns_2_on_empty PASSED [ 96%]
> ../nipype/utils/tests/test_cmd.py::TestNipypeCMD::test_main_returns_0_on_help PASSED [ 96%]
> ../nipype/utils/tests/test_cmd.py::TestNipypeCMD::test_list_nipy_interfacesp PASSED [ 96%]
> ../nipype/utils/tests/test_config.py::test_display_parse[:12] PASSED [ 96%]
> ../nipype/utils/tests/test_config.py::test_display_parse[localhost:12] PASSED [ 96%]
> ../nipype/utils/tests/test_config.py::test_display_parse[localhost:12.1] PASSED [ 96%]
> ../nipype/utils/tests/test_config.py::test_display_config[0] PASSED [ 96%]
> ../nipype/utils/tests/test_config.py::test_display_config[1] PASSED [ 96%]
> ../nipype/utils/tests/test_config.py::test_display_config[2] PASSED [ 96%]
> ../nipype/utils/tests/test_config.py::test_display_config[3] PASSED [ 96%]
> ../nipype/utils/tests/test_config.py::test_display_config[4] PASSED [ 96%]
> ../nipype/utils/tests/test_config.py::test_display_system[0] PASSED [ 96%]
> ../nipype/utils/tests/test_config.py::test_display_system[1] PASSED [ 96%]
> ../nipype/utils/tests/test_config.py::test_display_system[2] PASSED [ 96%]
> ../nipype/utils/tests/test_config.py::test_display_system[3] PASSED [ 96%]
> ../nipype/utils/tests/test_config.py::test_display_system[4] PASSED [ 96%]
> ../nipype/utils/tests/test_config.py::test_display_config_and_system PASSED [ 96%]
> ../nipype/utils/tests/test_config.py::test_display_noconfig_nosystem_patched PASSED [ 97%]
> ../nipype/utils/tests/test_config.py::test_display_empty_patched PASSED [ 97%]
> ../nipype/utils/tests/test_config.py::test_display_noconfig_nosystem_patched_oldxvfbwrapper PASSED [ 97%]
> ../nipype/utils/tests/test_config.py::test_display_empty_patched_oldxvfbwrapper PASSED [ 97%]
> ../nipype/utils/tests/test_config.py::test_display_noconfig_nosystem_notinstalled PASSED [ 97%]
> ../nipype/utils/tests/test_config.py::test_display_empty_notinstalled PASSED [ 97%]
> ../nipype/utils/tests/test_config.py::test_display_noconfig_nosystem_installed SKIPPED [ 97%]
> ../nipype/utils/tests/test_config.py::test_display_empty_installed SKIPPED [ 97%]
> ../nipype/utils/tests/test_config.py::test_display_empty_macosx PASSED [ 97%]
> ../nipype/utils/tests/test_config.py::test_cwd_cached PASSED [ 97%]
> ../nipype/utils/tests/test_config.py::test_debug_mode PASSED [ 97%]
> ../nipype/utils/tests/test_docparse.py::test_rev_opt_map PASSED [ 97%]
> ../nipype/utils/tests/test_docparse.py::test_build_doc PASSED [ 97%]
> ../nipype/utils/tests/test_docparse.py::test_insert_doc PASSED [ 97%]
> ../nipype/utils/tests/test_filemanip.py::test_split_filename[foo.nii-split0] PASSED [ 97%]
> ../nipype/utils/tests/test_filemanip.py::test_split_filename[foo.nii.gz-split1] PASSED [ 97%]
> ../nipype/utils/tests/test_filemanip.py::test_split_filename[foo.niml.dset-split2] PASSED [ 97%]
> ../nipype/utils/tests/test_filemanip.py::test_split_filename[/usr/local/foo.nii.gz-split3] PASSED [ 97%]
> ../nipype/utils/tests/test_filemanip.py::test_split_filename[../usr/local/foo.nii-split4] PASSED [ 97%]
> ../nipype/utils/tests/test_filemanip.py::test_split_filename[/usr/local/foo.a.b.c.d-split5] PASSED [ 97%]
> ../nipype/utils/tests/test_filemanip.py::test_split_filename[/usr/local/-split6] PASSED [ 97%]
> ../nipype/utils/tests/test_filemanip.py::test_fname_presuffix PASSED [ 97%]
> ../nipype/utils/tests/test_filemanip.py::test_fnames_presuffix PASSED [ 97%]
> ../nipype/utils/tests/test_filemanip.py::test_hash_rename[foobar.nii-foobar_0xabc123.nii] PASSED [ 97%]
> ../nipype/utils/tests/test_filemanip.py::test_hash_rename[foobar.nii.gz-foobar_0xabc123.nii.gz] PASSED [ 97%]
> ../nipype/utils/tests/test_filemanip.py::test_check_forhash PASSED [ 97%]
> ../nipype/utils/tests/test_filemanip.py::test_copyfile PASSED [ 97%]
> ../nipype/utils/tests/test_filemanip.py::test_copyfile_true PASSED [ 97%]
> ../nipype/utils/tests/test_filemanip.py::test_copyfiles PASSED [ 97%]
> ../nipype/utils/tests/test_filemanip.py::test_linkchain PASSED [ 97%]
> ../nipype/utils/tests/test_filemanip.py::test_recopy PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_copyfallback SKIPPED (...) [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_get_related_files PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_get_related_files_noninclusive PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_ensure_list[foo.nii-expected0] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_ensure_list[filename1-expected1] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_ensure_list[filename2-expected2] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_ensure_list[12.34-None] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_simplify_list[list0-foo.nii] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_simplify_list[list1-expected1] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_check_depends PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_json PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_related_files[/path/test.img-3-expected_files0] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_related_files[/path/test.hdr-3-expected_files1] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_related_files[/path/test.BRIK-2-expected_files2] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_related_files[/path/test.HEAD-2-expected_files3] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_related_files[/path/foo.nii-2-expected_files4] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_parse_mount_table[sysfs on /sys type sysfs (rw,nosuid,nodev,noexec,relatime)\nproc on /proc type proc (rw,nosuid,nodev,noexec,relatime)\nudev on /dev type devtmpfs (rw,nosuid,relatime,size=8121732k,nr_inodes=2030433,mode=755)\ndevpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000)\ntmpfs on /run type tmpfs (rw,nosuid,noexec,relatime,size=1628440k,mode=755)\n/dev/nvme0n1p2 on / type ext4 (rw,relatime,errors=remount-ro,data=ordered)\nsecurityfs on /sys/kernel/security type securityfs (rw,nosuid,nodev,noexec,relatime)\ntmpfs on /dev/shm type tmpfs (rw,nosuid,nodev)\ntmpfs on /sys/fs/cgroup type tmpfs (ro,nosuid,nodev,noexec,mode=755)\ncgroup on /sys/fs/cgroup/systemd type cgroup (rw,nosuid,nodev,noexec,relatime,xattr,release_agent=/lib/systemd/systemd-cgroups-agent,name=systemd)\npstore on /sys/fs/pstore type pstore (rw,nosuid,nodev,noexec,relatime)\nefivarfs on /sys/firmware/efi/efivars type efivarfs (rw,nosuid,nodev,noexec,relatime)\ncgroup on /sys/fs/cgroup/cpu,cpuacct type cgroup (rw,nosuid,nodev,noexec,relatime,cpu,cpuacct)\ncgroup on /sys/fs/cgroup/freezer type cgroup (rw,nosuid,nodev,noexec,relatime,freezer)\ncgroup on /sys/fs/cgroup/pids type cgroup (rw,nosuid,nodev,noexec,relatime,pids)\ncgroup on /sys/fs/cgroup/cpuset type cgroup (rw,nosuid,nodev,noexec,relatime,cpuset)\nsystemd-1 on /proc/sys/fs/binfmt_misc type autofs (rw,relatime,fd=26,pgrp=1,timeout=0,minproto=5,maxproto=5,direct)\nhugetlbfs on /dev/hugepages type hugetlbfs (rw,relatime)\ndebugfs on /sys/kernel/debug type debugfs (rw,relatime)\nmqueue on /dev/mqueue type mqueue (rw,relatime)\nfusectl on /sys/fs/fuse/connections type fusectl (rw,relatime)\n/dev/nvme0n1p1 on /boot/efi type vfat (rw,relatime,fmask=0077,dmask=0077,codepage=437,iocharset=iso8859-1,shortname=mixed,errors=remount-ro)\n/dev/nvme0n1p2 on /var/lib/docker/aufs type ext4 (rw,relatime,errors=remount-ro,data=ordered)\ngvfsd-fuse on /run/user/1002/gvfs type fuse.gvfsd-fuse (rw,nosuid,nodev,relatime,user_id=1002,group_id=1002)\n-0-expected0] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_parse_mount_table[/dev/disk2 on / (hfs, local, journaled)\ndevfs on /dev (devfs, local, nobrowse)\nmap -hosts on /net (autofs, nosuid, automounted, nobrowse)\nmap auto_home on /home (autofs, automounted, nobrowse)\nmap -fstab on /Network/Servers (autofs, automounted, nobrowse)\n/dev/disk3s2 on /Volumes/MyBookData (hfs, local, nodev, nosuid, journaled)\nafni:/elrond0 on /Volumes/afni (nfs)\nafni:/var/www/INCOMING on /Volumes/INCOMING (nfs)\nafni:/fraid on /Volumes/afni (nfs, asynchronous)\nboromir:/raid.bot on /Volumes/raid.bot (nfs)\nelros:/volume2/AFNI_SHARE on /Volumes/AFNI_SHARE (nfs)\nmap -static on /Volumes/safni (autofs, automounted, nobrowse)\nmap -static on /Volumes/raid.top (autofs, automounted, nobrowse)\n/dev/disk1s3 on /Volumes/Boot OS X (hfs, local, journaled, nobrowse)\n-0-expected1] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_parse_mount_table[-1-expected2] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_parse_mount_table[sysfs on /sys type sysfs (rw,nosuid,nodev,noexec,relatime)\nproc on /proc type proc (rw,nosuid,nodev,noexec,relatime)\nudev on /dev type devtmpfs (rw,nosuid,relatime,size=8121732k,nr_inodes=2030433,mode=755)\ndevpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000)\ntmpfs on /run type tmpfs (rw,nosuid,noexec,relatime,size=1628440k,mode=755)\n/dev/nvme0n1p2 on / type ext4 (rw,relatime,errors=remount-ro,data=ordered)\nsecurityfs on /sys/kernel/security type securityfs (rw,nosuid,nodev,noexec,relatime)\ntmpfs on /dev/shm type tmpfs (rw,nosuid,nodev)\ntmpfs on /sys/fs/cgroup type tmpfs (ro,nosuid,nodev,noexec,mode=755)\ncgroup on /sys/fs/cgroup/systemd type cgroup (rw,nosuid,nodev,noexec,relatime,xattr,release_agent=/lib/systemd/systemd-cgroups-agent,name=systemd)\npstore on /sys/fs/pstore type pstore (rw,nosuid,nodev,noexec,relatime)\nefivarfs on /sys/firmware/efi/efivars type efivarfs (rw,nosuid,nodev,noexec,relatime)\ncgroup on /sys/fs/cgroup/cpu,cpuacct type cgroup (rw,nosuid,nodev,noexec,relatime,cpu,cpuacct)\ncgroup on /sys/fs/cgroup/freezer type cgroup (rw,nosuid,nodev,noexec,relatime,freezer)\ncgroup on /sys/fs/cgroup/pids type cgroup (rw,nosuid,nodev,noexec,relatime,pids)\ncgroup on /sys/fs/cgroup/cpuset type cgroup (rw,nosuid,nodev,noexec,relatime,cpuset)\nsystemd-1 on /proc/sys/fs/binfmt_misc type autofs (rw,relatime,fd=26,pgrp=1,timeout=0,minproto=5,maxproto=5,direct)\nhugetlbfs on /dev/hugepages type hugetlbfs (rw,relatime)\ndebugfs on /sys/kernel/debug type debugfs (rw,relatime)\nmqueue on /dev/mqueue type mqueue (rw,relatime)\nfusectl on /sys/fs/fuse/connections type fusectl (rw,relatime)\n/dev/nvme0n1p1 on /boot/efi type vfat (rw,relatime,fmask=0077,dmask=0077,codepage=437,iocharset=iso8859-1,shortname=mixed,errors=remount-ro)\n/dev/nvme0n1p2 on /var/lib/docker/aufs type ext4 (rw,relatime,errors=remount-ro,data=ordered)\ngvfsd-fuse on /run/user/1002/gvfs type fuse.gvfsd-fuse (rw,nosuid,nodev,relatime,user_id=1002,group_id=1002)\n-0-expected3] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_parse_mount_table[/dev/disk2 on / (hfs, local, journaled)\ndevfs on /dev (devfs, local, nobrowse)\nafni:/elrond0 on /Volumes/afni (cifs)\nafni:/var/www/INCOMING on /Volumes/INCOMING (nfs)\nafni:/fraid on /Volumes/afni/fraid (nfs, asynchronous)\nboromir:/raid.bot on /Volumes/raid.bot (nfs)\nelros:/volume2/AFNI_SHARE on /Volumes/AFNI_SHARE (nfs)\n-0-expected4] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_parse_mount_table[overlay on / type overlay (rw,relatime,lowerdir=/var/lib/docker/overlay2/l/26UTYITLF24YE7KEGTMHUNHPPG:/var/lib/docker/overlay2/l/SWGNP3T2EEB4CNBJFN3SDZLXHP,upperdir=/var/lib/docker/overlay2/a4c54ab1aa031bb5a14a424abd655510521e183ee4fa4158672e8376c89df394/diff,workdir=/var/lib/docker/overlay2/a4c54ab1aa031bb5a14a424abd655510521e183ee4fa4158672e8376c89df394/work)\nproc on /proc type proc (rw,nosuid,nodev,noexec,relatime)\ntmpfs on /dev type tmpfs (rw,nosuid,size=65536k,mode=755)\ndevpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=666)\nsysfs on /sys type sysfs (ro,nosuid,nodev,noexec,relatime)\ntmpfs on /sys/fs/cgroup type tmpfs (ro,nosuid,nodev,noexec,relatime,mode=755)\ncpuset on /sys/fs/cgroup/cpuset type cgroup (ro,nosuid,nodev,noexec,relatime,cpuset)\ncpu on /sys/fs/cgroup/cpu type cgroup (ro,nosuid,nodev,noexec,relatime,cpu)\ncpuacct on /sys/fs/cgroup/cpuacct type cgroup (ro,nosuid,nodev,noexec,relatime,cpuacct)\nblkio on /sys/fs/cgroup/blkio type cgroup (ro,nosuid,nodev,noexec,relatime,blkio)\nmemory on /sys/fs/cgroup/memory type cgroup (ro,nosuid,nodev,noexec,relatime,memory)\ndevices on /sys/fs/cgroup/devices type cgroup (ro,nosuid,nodev,noexec,relatime,devices)\nfreezer on /sys/fs/cgroup/freezer type cgroup (ro,nosuid,nodev,noexec,relatime,freezer)\nnet_cls on /sys/fs/cgroup/net_cls type cgroup (ro,nosuid,nodev,noexec,relatime,net_cls)\nperf_event on /sys/fs/cgroup/perf_event type cgroup (ro,nosuid,nodev,noexec,relatime,perf_event)\nnet_prio on /sys/fs/cgroup/net_prio type cgroup (ro,nosuid,nodev,noexec,relatime,net_prio)\nhugetlb on /sys/fs/cgroup/hugetlb type cgroup (ro,nosuid,nodev,noexec,relatime,hugetlb)\npids on /sys/fs/cgroup/pids type cgroup (ro,nosuid,nodev,noexec,relatime,pids)\ncgroup on /sys/fs/cgroup/systemd type cgroup (ro,nosuid,nodev,noexec,relatime,name=systemd)\nmqueue on /dev/mqueue type mqueue (rw,nosuid,nodev,noexec,relatime)\n/10.0.75.1/C on /data type cifs (rw,relatime,vers=3.02,sec=ntlmsspi,cache=strict,username=filo,domain=MSI,uid=0,noforceuid,gid=0,noforcegid,addr=10.0.75.1,file_mode=0755,dir_mode=0755,iocharset=utf8,nounix,serverino,mapposix,nobrl,mfsymlinks,noperm,rsize=1048576,wsize=1048576,echo_interval=60,actimeo=1)\n/dev/sda1 on /etc/resolv.conf type ext4 (rw,relatime,data=ordered)\n/dev/sda1 on /etc/hostname type ext4 (rw,relatime,data=ordered)\n/dev/sda1 on /etc/hosts type ext4 (rw,relatime,data=ordered)\nshm on /dev/shm type tmpfs (rw,nosuid,nodev,noexec,relatime,size=65536k)\ndevpts on /dev/console type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=666)\nproc on /proc/bus type proc (ro,relatime)\nproc on /proc/fs type proc (ro,relatime)\nproc on /proc/irq type proc (ro,relatime)\nproc on /proc/sys type proc (ro,relatime)\nproc on /proc/sysrq-trigger type proc (ro,relatime)\ntmpfs on /proc/kcore type tmpfs (rw,nosuid,size=65536k,mode=755)\ntmpfs on /proc/timer_list type tmpfs (rw,nosuid,size=65536k,mode=755)\ntmpfs on /proc/sched_debug type tmpfs (rw,nosuid,size=65536k,mode=755)\ntmpfs on /proc/scsi type tmpfs (ro,relatime)\ntmpfs on /sys/firmware type tmpfs (ro,relatime)\n-0-expected5] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_parse_mount_table[/proc on /proc type proc (rw,relatime)\nsysfs on /sys type sysfs (rw,nosuid,nodev,noexec,relatime)\ntmpfs on /dev/shm type tmpfs (rw,relatime)\ndevpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=666)\n\ndevpts on /dev/ptmx type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=666)\n\n-0-expected6] PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_cifs_check PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_indirectory PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_pklization PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_versioned_pklization PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_unversioned_pklization PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_path_strict_resolve PASSED [ 98%]
> ../nipype/utils/tests/test_filemanip.py::test_pickle[True] PASSED [ 99%]
> ../nipype/utils/tests/test_filemanip.py::test_pickle[False] PASSED [ 99%]
> ../nipype/utils/tests/test_filemanip.py::test_write_rst_list[- \n\n] PASSED [ 99%]
> ../nipype/utils/tests/test_filemanip.py::test_write_rst_list[A string- A string\n\n] PASSED [ 99%]
> ../nipype/utils/tests/test_filemanip.py::test_write_rst_list[items2- A list\n Of strings\n\n] PASSED [ 99%]
> ../nipype/utils/tests/test_filemanip.py::test_write_rst_list[None-TypeError] PASSED [ 99%]
> ../nipype/utils/tests/test_filemanip.py::test_emptydirs_dangling_nfs PASSED [ 99%]
> ../nipype/utils/tests/test_functions.py::test_func_to_str PASSED [ 99%]
> ../nipype/utils/tests/test_functions.py::test_func_to_str_err PASSED [ 99%]
> ../nipype/utils/tests/test_functions.py::test_func_string PASSED [ 99%]
> ../nipype/utils/tests/test_functions.py::test_func_print PASSED [ 99%]
> ../nipype/utils/tests/test_imagemanip.py::test_copy_header[True] PASSED [ 99%]
> ../nipype/utils/tests/test_imagemanip.py::test_copy_header[False] PASSED [ 99%]
> ../nipype/utils/tests/test_misc.py::test_cont_to_str PASSED [ 99%]
> ../nipype/utils/tests/test_misc.py::test_str2bool[yes-True] PASSED [ 99%]
> ../nipype/utils/tests/test_misc.py::test_str2bool[true-True] PASSED [ 99%]
> ../nipype/utils/tests/test_misc.py::test_str2bool[t-True] PASSED [ 99%]
> ../nipype/utils/tests/test_misc.py::test_str2bool[1-True] PASSED [ 99%]
> ../nipype/utils/tests/test_misc.py::test_str2bool[no-False] PASSED [ 99%]
> ../nipype/utils/tests/test_misc.py::test_str2bool[false-False] PASSED [ 99%]
> ../nipype/utils/tests/test_misc.py::test_str2bool[n-False] PASSED [ 99%]
> ../nipype/utils/tests/test_misc.py::test_str2bool[f-False] PASSED [ 99%]
> ../nipype/utils/tests/test_misc.py::test_str2bool[0-False] PASSED [ 99%]
> ../nipype/utils/tests/test_misc.py::test_flatten PASSED [ 99%]
> ../nipype/utils/tests/test_misc.py::test_rgetcwd PASSED [ 99%]
> ../nipype/utils/tests/test_misc.py::test_dict_diff PASSED [ 99%]
> ../nipype/utils/tests/test_nipype2boutiques.py::test_generate PASSED [ 99%]
> ../nipype/utils/tests/test_provenance.py::test_provenance PASSED [ 99%]
> ../nipype/utils/tests/test_provenance.py::test_provenance_exists PASSED [ 99%]
> ../nipype/utils/tests/test_provenance.py::test_safe_encode PASSED [100%]
>
> =================================== FAILURES ===================================
> _____________________ test_BaseInterface_load_save_inputs ______________________
>
> tmpdir = local('/tmp/pytest-of-user42/pytest-12/test_BaseInterface_load_save_i0')
>
> def test_BaseInterface_load_save_inputs(tmpdir):
> tmp_json = tmpdir.join("settings.json").strpath
>
> class InputSpec(nib.TraitedSpec):
> input1 = nib.traits.Int()
> input2 = nib.traits.Float()
> input3 = nib.traits.Bool()
> input4 = nib.traits.Str()
>
> class DerivedInterface(nib.BaseInterface):
> input_spec = InputSpec
>
> def __init__(self, **inputs):
> super(DerivedInterface, self).__init__(**inputs)
>
> inputs_dict = {"input1": 12, "input3": True, "input4": "some string"}
> bif = DerivedInterface(**inputs_dict)
> bif.save_inputs_to_json(tmp_json)
> bif2 = DerivedInterface()
> bif2.load_inputs_from_json(tmp_json)
> assert bif2.inputs.get_traitsfree() == inputs_dict
>
> bif3 = DerivedInterface(from_file=tmp_json)
> assert bif3.inputs.get_traitsfree() == inputs_dict
>
> inputs_dict2 = inputs_dict.copy()
> inputs_dict2.update({"input4": "some other string"})
> bif4 = DerivedInterface(from_file=tmp_json, input4=inputs_dict2["input4"])
> assert bif4.inputs.get_traitsfree() == inputs_dict2
>
> bif5 = DerivedInterface(input4=inputs_dict2["input4"])
> bif5.load_inputs_from_json(tmp_json, overwrite=False)
> assert bif5.inputs.get_traitsfree() == inputs_dict2
>
> bif6 = DerivedInterface(input4=inputs_dict2["input4"])
> bif6.load_inputs_from_json(tmp_json)
> assert bif6.inputs.get_traitsfree() == inputs_dict
>
> # test get hashval in a complex interface
> from nipype.interfaces.ants import Registration
>
> settings = example_data(example_data("smri_ants_registration_settings.json"))
> with open(settings) as setf:
> data_dict = json.load(setf)
>
> tsthash = Registration()
> > tsthash.load_inputs_from_json(settings)
>
> /<<PKGBUILDDIR>>/nipype/interfaces/base/tests/test_core.py:153:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> /<<PKGBUILDDIR>>/nipype/interfaces/base/core.py:489: in load_inputs_from_json
> setattr(self.inputs, key, inputs_dict[key])
> /usr/lib/python3/dist-packages/traits/trait_types.py:2695: in validate
> return TraitListObject(self, object, name, value)
> /usr/lib/python3/dist-packages/traits/trait_list_object.py:584: in __init__
> super().__init__(
> /usr/lib/python3/dist-packages/traits/trait_list_object.py:213: in __init__
> super().__init__(self.item_validator(item) for item in iterable)
> /usr/lib/python3/dist-packages/traits/trait_list_object.py:213: in <genexpr>
> super().__init__(self.item_validator(item) for item in iterable)
> /usr/lib/python3/dist-packages/traits/trait_list_object.py:867: in _item_validator
> return trait_validator(object, self.name, value)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> self = <traits.trait_handlers.TraitCompound object at 0x7f2bd8a24d50>
> object =
> args = <undefined>
> collapse_output_transforms = False
> convergence_threshold = [1e-06]
> convergence_window_size = [20, ... = True
> verbose = False
> winsorize_lower_quantile = 0.0
> winsorize_upper_quantile = 1.0
> write_composite_transform = True
>
> name = 'transform_parameters', value = [0.1]
>
> def error(self, object, name, value):
> """Raises a TraitError exception.
>
> This method is called by the validate() method when an assigned value
> is not valid. Raising a TraitError exception either notifies the user
> of the problem, or, in the case of compound traits, provides a chance
> for another trait handler to handle to validate the value.
>
> Parameters
> ----------
> object : object
> The object whose attribute is being assigned.
> name : str
> The name of the attribute being assigned.
> value : object
> The proposed new value for the attribute.
> """
> > raise TraitError(
> object, name, self.full_info(object, name, value), value
> )
> E traits.trait_errors.TraitError: Each element of the 'transform_parameters' trait of a RegistrationInputSpec instance must be a tuple of the form: (a float) or a tuple of the form: (a float, a float, a float) or a tuple of the form: (a float, an integer, an integer, an integer) or a tuple of the form: (a float, an integer, a float, a float, a float, a float) or a tuple of the form: (a float, a float, a float, an integer) or a tuple of the form: (a float, an integer, an integer, an integer, an integer), but a value of [0.1] <class 'list'> was specified.
>
> /usr/lib/python3/dist-packages/traits/base_trait_handler.py:74: TraitError
> _________ [doctest] nipype.interfaces.fsl.model.MultipleRegressDesign __________
> 1491 Please see `FSL documentation
> 1492 <http://www.fmrib.ox.ac.uk/fsl/feat5/detail.html#higher>`_
> 1493 for more details on model specification for higher level analysis.
> 1494
> 1495 Examples
> 1496 --------
> 1497
> 1498 >>> from nipype.interfaces.fsl import MultipleRegressDesign
> 1499 >>> model = MultipleRegressDesign()
> 1500 >>> model.inputs.contrasts = [['group mean', 'T',['reg1'],[1]]]
> UNEXPECTED EXCEPTION: TraitError("Each element of the 'contrasts' trait of a MultipleRegressDesignInputSpec instance must be a tuple of the form: (a string, 'T', a list of items which are a string, a list of items which are a float) or a tuple of the form: (a string, 'F', a list of items which are a tuple of the form: (a string, 'T', a list of items which are a string, a list of items which are a float)), but a value of ['group mean', 'T', ['reg1'], [1]] <class 'list'> was specified.")
> Traceback (most recent call last):
> File "/usr/lib/python3.11/doctest.py", line 1355, in __run
> exec(compile(example.source, filename, "single",
> File "<doctest nipype.interfaces.fsl.model.MultipleRegressDesign[2]>", line 1, in <module>
> File "/usr/lib/python3/dist-packages/traits/trait_types.py", line 2695, in validate
> return TraitListObject(self, object, name, value)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "/usr/lib/python3/dist-packages/traits/trait_list_object.py", line 584, in __init__
> super().__init__(
> File "/usr/lib/python3/dist-packages/traits/trait_list_object.py", line 213, in __init__
> super().__init__(self.item_validator(item) for item in iterable)
> File "/usr/lib/python3/dist-packages/traits/trait_list_object.py", line 213, in <genexpr>
> super().__init__(self.item_validator(item) for item in iterable)
> ^^^^^^^^^^^^^^^^^^^^^^^^^
> File "/usr/lib/python3/dist-packages/traits/trait_list_object.py", line 867, in _item_validator
> return trait_validator(object, self.name, value)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "/usr/lib/python3/dist-packages/traits/base_trait_handler.py", line 74, in error
> raise TraitError(
> traits.trait_errors.TraitError: Each element of the 'contrasts' trait of a MultipleRegressDesignInputSpec instance must be a tuple of the form: (a string, 'T', a list of items which are a string, a list of items which are a float) or a tuple of the form: (a string, 'F', a list of items which are a tuple of the form: (a string, 'T', a list of items which are a string, a list of items which are a float)), but a value of ['group mean', 'T', ['reg1'], [1]] <class 'list'> was specified.
> /<<PKGBUILDDIR>>/nipype/interfaces/fsl/model.py:1500: UnexpectedException
> =============================== warnings summary ===============================
> ../../../../usr/lib/python3/dist-packages/traits/observation/_generated_parser.py:258
> /usr/lib/python3/dist-packages/traits/observation/_generated_parser.py:258: DeprecationWarning: module 'sre_parse' is deprecated
> import sre_parse
>
> ../../../../usr/lib/python3/dist-packages/traits/observation/_generated_parser.py:259
> /usr/lib/python3/dist-packages/traits/observation/_generated_parser.py:259: DeprecationWarning: module 'sre_constants' is deprecated
> import sre_constants
>
> ../../../../usr/lib/python3/dist-packages/_pytest/config/__init__.py:1373
> /usr/lib/python3/dist-packages/_pytest/config/__init__.py:1373: PytestConfigWarning: Unknown config option: env
>
> self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
>
> ../nipype/interfaces/dcmstack.py:11
> /<<PKGBUILDDIR>>/nipype/interfaces/dcmstack.py:11: DeprecationWarning: 'imghdr' is deprecated and slated for removal in Python 3.13
> import imghdr
>
> ../nipype/interfaces/base/tests/test_support.py:7
> /<<PKGBUILDDIR>>/nipype/interfaces/base/tests/test_support.py:7: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
> from pkg_resources import resource_filename as pkgrf
>
> ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871
> /usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('mpl_toolkits')`.
> Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
> declare_namespace(pkg)
>
> ../nipype/interfaces/freesurfer/base.py:62
> ../nipype/interfaces/freesurfer/base.py:62
> ../nipype/interfaces/freesurfer/base.py:62
> interfaces/freesurfer/preprocess.py::nipype.interfaces.freesurfer.preprocess.BBRegister
> interfaces/freesurfer/preprocess.py::nipype.interfaces.freesurfer.preprocess.ReconAll
> interfaces/freesurfer/preprocess.py::nipype.interfaces.freesurfer.preprocess.ReconAll
> interfaces/freesurfer/tests/test_BBRegister.py::test_BBRegister_inputs
> /<<PKGBUILDDIR>>/nipype/interfaces/freesurfer/base.py:62: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
> return LooseVersion("0.0.0")
>
> ../nipype/interfaces/freesurfer/preprocess.py:1109
> /<<PKGBUILDDIR>>/nipype/interfaces/freesurfer/preprocess.py:1109: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
> if Info.looseversion() < LooseVersion("6.0.0"):
>
> ../nipype/interfaces/freesurfer/preprocess.py:1829
> /<<PKGBUILDDIR>>/nipype/interfaces/freesurfer/preprocess.py:1829: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
> if LooseVersion("0.0.0") < Info.looseversion() < LooseVersion("6.0.0"):
>
> ../nipype/interfaces/tests/test_image.py:12
> ../nipype/interfaces/tests/test_image.py:12
> /<<PKGBUILDDIR>>/nipype/interfaces/tests/test_image.py:12: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
> nibabel24 = LooseVersion(nb.__version__) >= LooseVersion("2.4.0")
>
> ../nipype/pipeline/engine/tests/test_nodes.py:320
> /<<PKGBUILDDIR>>/nipype/pipeline/engine/tests/test_nodes.py:320: PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
> @pytest.mark.timeout(30)
>
> ../nipype/pipeline/plugins/tests/test_oar.py:33
> /<<PKGBUILDDIR>>/nipype/pipeline/plugins/tests/test_oar.py:33: PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
> @pytest.mark.timeout(60)
>
> ../nipype/pipeline/plugins/tests/test_pbs.py:33
> /<<PKGBUILDDIR>>/nipype/pipeline/plugins/tests/test_pbs.py:33: PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
> @pytest.mark.timeout(60)
>
> ../../../../usr/lib/python3/dist-packages/babel/messages/catalog.py:13
> /usr/lib/python3/dist-packages/babel/messages/catalog.py:13: DeprecationWarning: 'cgi' is deprecated and slated for removal in Python 3.13
> from cgi import parse_header
>
> ../nipype/utils/tests/test_provenance.py:18
> /<<PKGBUILDDIR>>/nipype/utils/tests/test_provenance.py:18: PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
> @pytest.mark.timeout(60)
>
> ../nipype/utils/tests/test_provenance.py:31
> /<<PKGBUILDDIR>>/nipype/utils/tests/test_provenance.py:31: PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
> @pytest.mark.timeout(60)
>
> ../nipype/workflows/__init__.py:28
> /<<PKGBUILDDIR>>/nipype/workflows/__init__.py:28: UserWarning: Nipype 1 workflows have been moved to the niflow-nipype1-workflows package. pip install niflow-nipype1-workflows to continue using them.
> warnings.warn(" ".join(_msg))
>
> algorithms/tests/test_CompCor.py::TestCompCor::test_tcompcor_asymmetric_dim
> /<<PKGBUILDDIR>>/nipype/algorithms/confounds.py:1460: RuntimeWarning: invalid value encountered in divide
> variance_explained = (s**2) / np.sum(s**2)
>
> interfaces/image.py::nipype.interfaces.image.Reorient
> interfaces/image.py::nipype.interfaces.image.Reorient
> interfaces/image.py::nipype.interfaces.image.Reorient
> interfaces/image.py::nipype.interfaces.image.Reorient
> /<<PKGBUILDDIR>>/nipype/interfaces/image.py:201: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
> if LooseVersion(nb.__version__) >= LooseVersion("2.4.0"):
>
> interfaces/ants/utils.py::nipype.interfaces.ants.utils.ImageMath
> /<<PKGBUILDDIR>>/nipype/interfaces/ants/utils.py:215: UserWarning: copy_header cannot be updated to True with PadImage as operation.
> warn(
>
> interfaces/base/tests/test_core.py: 15 warnings
> interfaces/nipy/preprocess.py: 2 warnings
> /<<PKGBUILDDIR>>/nipype/interfaces/base/core.py:297: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
> version = LooseVersion(str(self.version))
>
> interfaces/base/tests/test_core.py: 15 warnings
> interfaces/nipy/preprocess.py: 2 warnings
> /<<PKGBUILDDIR>>/nipype/interfaces/base/core.py:299: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
> min_ver = LooseVersion(str(trait_object.traits()[name].min_ver))
>
> interfaces/base/tests/test_core.py: 17 warnings
> /<<PKGBUILDDIR>>/nipype/interfaces/base/core.py:326: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
> version = LooseVersion(str(self.version))
>
> interfaces/base/tests/test_core.py: 17 warnings
> /<<PKGBUILDDIR>>/nipype/interfaces/base/core.py:328: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
> max_ver = LooseVersion(str(trait_object.traits()[name].max_ver))
>
> interfaces/base/tests/test_core.py: 16 warnings
> pipeline/engine/tests/test_nodes.py: 2 warnings
> utils/tests/test_provenance.py: 4 warnings
> /<<PKGBUILDDIR>>/nipype/utils/subprocess.py:34: DeprecationWarning: 'locale.getdefaultlocale' is deprecated and slated for removal in Python 3.15. Use setlocale(), getencoding() and getlocale() instead.
> self.default_encoding = locale.getdefaultlocale()[1] or "UTF-8"
>
> interfaces/base/tests/test_core.py::test_CommandLine_output
> interfaces/base/tests/test_core.py::test_CommandLine_output
> interfaces/base/tests/test_core.py::test_CommandLine_output
> interfaces/base/tests/test_core.py::test_CommandLine_output
> interfaces/base/tests/test_core.py::test_CommandLine_output
> interfaces/base/tests/test_core.py::test_CommandLine_output
> interfaces/base/tests/test_core.py::test_CommandLine_output
> utils/filemanip.py::nipype.utils.filemanip.read_stream
> /<<PKGBUILDDIR>>/nipype/utils/filemanip.py:696: DeprecationWarning: 'locale.getdefaultlocale' is deprecated and slated for removal in Python 3.15. Use setlocale(), getencoding() and getlocale() instead.
> default_encoding = encoding or locale.getdefaultlocale()[1] or "UTF-8"
>
> interfaces/freesurfer/preprocess.py::nipype.interfaces.freesurfer.preprocess.BBRegister
> interfaces/freesurfer/tests/test_BBRegister.py::test_BBRegister_inputs
> /<<PKGBUILDDIR>>/nipype/interfaces/freesurfer/base.py:179: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
> if ver > LooseVersion("0.0.0"):
>
> interfaces/freesurfer/preprocess.py::nipype.interfaces.freesurfer.preprocess.ReconAll
> interfaces/freesurfer/preprocess.py::nipype.interfaces.freesurfer.preprocess.ReconAll
> /<<PKGBUILDDIR>>/nipype/interfaces/freesurfer/preprocess.py:1686: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
> if ver > LooseVersion("0.0.0"):
>
> interfaces/freesurfer/tests/test_preprocess.py::test_FSVersion
> interfaces/freesurfer/tests/test_preprocess.py::test_FSVersion
> /<<PKGBUILDDIR>>/nipype/interfaces/freesurfer/tests/test_preprocess.py:197: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
> assert LooseVersion(freesurfer.preprocess.FSVersion) >= LooseVersion("0")
>
> interfaces/fsl/dti.py::nipype.interfaces.fsl.dti.ProbTrackX
> interfaces/fsl/dti.py::nipype.interfaces.fsl.dti.ProbTrackX2
> /<<PKGBUILDDIR>>/nipype/interfaces/fsl/dti.py:815: DeprecationWarning: Deprecated: Please use create_bedpostx_pipeline instead
> warnings.warn(
>
> interfaces/fsl/epi.py::nipype.interfaces.fsl.epi.EPIDeWarp
> /<<PKGBUILDDIR>>/nipype/interfaces/fsl/epi.py:1413: DeprecationWarning: Deprecated: Please use niflow.nipype1.workflows.dmri.preprocess.epi.sdc_fmb instead
> warnings.warn(
>
> interfaces/fsl/epi.py::nipype.interfaces.fsl.epi.EddyCorrect
> /<<PKGBUILDDIR>>/nipype/interfaces/fsl/epi.py:1519: DeprecationWarning: Deprecated: Please use nipype.interfaces.fsl.epi.Eddy instead
> warnings.warn(
>
> interfaces/nipy/utils.py::nipype.interfaces.nipy.utils.Similarity
> /<<PKGBUILDDIR>>/nipype/interfaces/nipy/utils.py:59: DeprecationWarning: This interface is deprecated since 0.10.0. Please use nipype.algorithms.metrics.Similarity
> warnings.warn(
>
> interfaces/nitime/tests/test_nitime.py::test_coherence_analysis
> /usr/lib/python3/dist-packages/nitime/analysis/coherence.py:200: RuntimeWarning: invalid value encountered in divide
> delay[i, j] = this_phase / (2 * np.pi * self.frequencies)
>
> interfaces/nitime/tests/test_nitime.py::test_coherence_analysis
> /usr/lib/python3/dist-packages/nitime/analysis/coherence.py:200: RuntimeWarning: divide by zero encountered in divide
> delay[i, j] = this_phase / (2 * np.pi * self.frequencies)
>
> pipeline/engine/tests/test_engine.py: 24 warnings
> <class 'networkx.utils.decorators.argmap'> compilation 13:5: PendingDeprecationWarning: nx.nx_pydot.write_dot depends on the pydot package, which hasknown issues and is not actively maintained. Consider usingnx.nx_agraph.write_dot instead.
>
> See https://github.com/networkx/networkx/issues/5723
>
> pipeline/engine/tests/test_engine.py: 24 warnings
> /usr/lib/python3/dist-packages/networkx/drawing/nx_pydot.py:51: PendingDeprecationWarning: nx.nx_pydot.to_pydot depends on the pydot package, which hasknown issues and is not actively maintained.
>
> See https://github.com/networkx/networkx/issues/5723
> P = to_pydot(G)
>
> utils/tests/test_misc.py::test_rgetcwd
> /<<PKGBUILDDIR>>/nipype/utils/misc.py:373: UserWarning: Current folder does not exist, replacing with "/tmp/pytest-of-user42/pytest-12/test_rgetcwd0" instead.
> warn('Current folder does not exist, replacing with "%s" instead.' % cwd)
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info ============================
> FAILED ../nipype/interfaces/base/tests/test_core.py::test_BaseInterface_load_save_inputs
> FAILED ../nipype/interfaces/fsl/model.py::nipype.interfaces.fsl.model.MultipleRegressDesign
> = 2 failed, 2723 passed, 243 skipped, 1 deselected, 5 xfailed, 190 warnings in 147.98s (0:02:27) =
> make[1]: *** [debian/rules:39: override_dh_auto_test] Error 1
The full build log is available from:
http://qa-logs.debian.net/2024/02/24/nipype_1.8.6-3_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240224;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240224&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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