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Published 20 hours ago • verified publisher icon DeepLabCut

Installing on Jetson Xavier AGX

Open darioringach opened this issue 4 years ago • 16 comments

All good until last step... and then:

(dlc-live) dario@dario-jetson:~$ pip install deeplabcut-live Collecting deeplabcut-live Downloading deeplabcut_live-1.0-py3-none-any.whl (28 kB) Collecting numpy<1.19.0 Downloading numpy-1.18.5.zip (5.4 MB) |████████████████████████████████| 5.4 MB 13.5 MB/s Installing build dependencies ... done Getting requirements to build wheel ... done Preparing wheel metadata ... done Collecting ruamel.yaml Downloading ruamel.yaml-0.16.13-py2.py3-none-any.whl (111 kB) |████████████████████████████████| 111 kB 9.9 MB/s Collecting pillow Downloading Pillow-8.1.2-cp36-cp36m-manylinux2014_aarch64.whl (2.1 MB) |████████████████████████████████| 2.1 MB 14.9 MB/s Collecting colorcet Downloading colorcet-2.0.6-py2.py3-none-any.whl (1.6 MB) |████████████████████████████████| 1.6 MB 15.5 MB/s Collecting opencv-python Downloading opencv_python-4.5.1.48-cp36-cp36m-manylinux2014_aarch64.whl (34.5 MB) |████████████████████████████████| 34.5 MB 22 kB/s Collecting tqdm Downloading tqdm-4.59.0-py2.py3-none-any.whl (74 kB) |████████████████████████████████| 74 kB 2.0 MB/s Collecting tables Downloading tables-3.6.1.tar.gz (4.6 MB) |████████████████████████████████| 4.6 MB 12.9 MB/s Collecting deeplabcut-live Downloading deeplabcut_live-0.0.3-py3-none-any.whl (39 kB) Collecting numpy Downloading numpy-1.19.5-cp36-cp36m-manylinux2014_aarch64.whl (12.4 MB) |████████████████████████████████| 12.4 MB 10.8 MB/s Collecting deeplabcut-live Downloading deeplabcut_live-0.0.2-py3-none-any.whl (42 kB) |████████████████████████████████| 42 kB 404 kB/s Downloading deeplabcut_live-0.0.1-py3-none-any.whl (29 kB) Downloading deeplabcut_live-0.0-py3-none-any.whl (39 kB) Collecting py-cpuinfo==5.0.0 Downloading py-cpuinfo-5.0.0.tar.gz (82 kB) |████████████████████████████████| 82 kB 221 kB/s Collecting pandas Downloading pandas-1.1.5-cp36-cp36m-manylinux2014_aarch64.whl (9.5 MB) |████████████████████████████████| 9.5 MB 9.4 MB/s Collecting pyct>=0.4.4 Downloading pyct-0.4.8-py2.py3-none-any.whl (15 kB) Collecting param>=1.7.0 Downloading param-1.10.1-py2.py3-none-any.whl (76 kB) |████████████████████████████████| 76 kB 3.8 MB/s Collecting pytz>=2017.2 Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB) |████████████████████████████████| 510 kB 14.2 MB/s Collecting python-dateutil>=2.7.3 Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB) |████████████████████████████████| 227 kB 14.5 MB/s Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting ruamel.yaml.clib>=0.1.2 Downloading ruamel.yaml.clib-0.2.2-cp36-cp36m-manylinux2014_aarch64.whl (540 kB) |████████████████████████████████| 540 kB 12.8 MB/s Collecting numexpr>=2.6.2 Downloading numexpr-2.7.3-cp36-cp36m-manylinux2014_aarch64.whl (481 kB) |████████████████████████████████| 481 kB 15.4 MB/s Using legacy 'setup.py install' for py-cpuinfo, since package 'wheel' is not installed. Using legacy 'setup.py install' for tables, since package 'wheel' is not installed. Installing collected packages: six, param, numpy, ruamel.yaml.clib, pytz, python-dateutil, pyct, numexpr, tqdm, tables, ruamel.yaml, py-cpuinfo, pillow, pandas, colorcet, deeplabcut-live Running setup.py install for tables ... error ERROR: Command errored out with exit status -4: command: /home/dario/dlc-live/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-p9_amnr6/tables_db97b7244bac4c15a79f2d6898028816/setup.py'"'"'; file='"'"'/tmp/pip-install-p9_amnr6/tables_db97b7244bac4c15a79f2d6898028816/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-wtlkb57w/install-record.txt --single-version-externally-managed --compile --install-headers /home/dario/dlc-live/include/site/python3.6/tables cwd: /tmp/pip-install-p9_amnr6/tables_db97b7244bac4c15a79f2d6898028816/ Complete output (188 lines): * Using Python 3.6.9 (default, Jan 26 2021, 15:33:00) * USE_PKGCONFIG: True * pkg-config header dirs for HDF5: /usr/include/hdf5/serial * pkg-config library dirs for HDF5: /usr/lib/aarch64-linux-gnu/hdf5/serial * Found HDF5 headers at /usr/include/hdf5/serial, library at /usr/lib/aarch64-linux-gnu/hdf5/serial. .. WARNING:: Could not find the HDF5 runtime. The HDF5 shared library was not found in the default library paths. In case of runtime problems, please remember to install it. /tmp/lzo_version_datesb8__dcy.c:1:1: warning: return type defaults to ‘int’ [-Wimplicit-int] main (int argc, char **argv) { ^~~~ /tmp/lzo_version_datesb8__dcy.c: In function ‘main’: /tmp/lzo_version_datesb8__dcy.c:2:5: warning: implicit declaration of function ‘lzo_version_date’ [-Wimplicit-function-declaration] lzo_version_date(); ^~~~~~~~~~~~~~~~ /usr/bin/ld: cannot find -llzo2 collect2: error: ld returned 1 exit status * Could not find LZO 2 headers and library; disabling support for it. /tmp/lzo_version_datewqm9562s.c:1:1: warning: return type defaults to ‘int’ [-Wimplicit-int] main (int argc, char **argv) { ^~~~ /tmp/lzo_version_datewqm9562s.c: In function ‘main’: /tmp/lzo_version_datewqm9562s.c:2:5: warning: implicit declaration of function ‘lzo_version_date’ [-Wimplicit-function-declaration] lzo_version_date(); ^~~~~~~~~~~~~~~~ /usr/bin/ld: cannot find -llzo collect2: error: ld returned 1 exit status * Could not find LZO 1 headers and library; disabling support for it. /tmp/BZ2_bzlibVersionr8ji2103.c:1:1: warning: return type defaults to ‘int’ [-Wimplicit-int] main (int argc, char **argv) { ^~~~ /tmp/BZ2_bzlibVersionr8ji2103.c: In function ‘main’: /tmp/BZ2_bzlibVersionr8ji2103.c:2:5: warning: implicit declaration of function ‘BZ2_bzlibVersion’ [-Wimplicit-function-declaration] BZ2_bzlibVersion(); ^~~~~~~~~~~~~~~~ /usr/bin/ld: cannot find -lbz2 collect2: error: ld returned 1 exit status * Could not find bzip2 headers and library; disabling support for it. /tmp/blosc_list_compressorsv4to05p7.c:1:1: warning: return type defaults to ‘int’ [-Wimplicit-int] main (int argc, char **argv) { ^~~~ /tmp/blosc_list_compressorsv4to05p7.c: In function ‘main’: /tmp/blosc_list_compressorsv4to05p7.c:2:5: warning: implicit declaration of function ‘blosc_list_compressors’ [-Wimplicit-function-declaration] blosc_list_compressors(); ^~~~~~~~~~~~~~~~~~~~~~ /usr/bin/ld: cannot find -lblosc collect2: error: ld returned 1 exit status * Could not find blosc headers and library; using internal sources. /usr/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'extra_require' warnings.warn(msg) running install running build running build_py creating build creating build/lib.linux-aarch64-3.6 creating build/lib.linux-aarch64-3.6/tables copying tables/idxutils.py -> build/lib.linux-aarch64-3.6/tables copying tables/leaf.py -> build/lib.linux-aarch64-3.6/tables copying tables/vlarray.py -> build/lib.linux-aarch64-3.6/tables copying tables/node.py -> build/lib.linux-aarch64-3.6/tables copying tables/flavor.py -> build/lib.linux-aarch64-3.6/tables copying tables/filters.py -> build/lib.linux-aarch64-3.6/tables copying tables/carray.py -> build/lib.linux-aarch64-3.6/tables copying tables/atom.py -> build/lib.linux-aarch64-3.6/tables copying tables/conditions.py -> build/lib.linux-aarch64-3.6/tables copying tables/parameters.py -> build/lib.linux-aarch64-3.6/tables copying tables/utils.py -> build/lib.linux-aarch64-3.6/tables copying tables/file.py -> build/lib.linux-aarch64-3.6/tables copying tables/registry.py -> build/lib.linux-aarch64-3.6/tables copying tables/indexes.py -> build/lib.linux-aarch64-3.6/tables copying tables/link.py -> build/lib.linux-aarch64-3.6/tables copying tables/init.py -> build/lib.linux-aarch64-3.6/tables copying tables/index.py -> build/lib.linux-aarch64-3.6/tables copying tables/earray.py -> build/lib.linux-aarch64-3.6/tables copying tables/array.py -> build/lib.linux-aarch64-3.6/tables copying tables/description.py -> build/lib.linux-aarch64-3.6/tables copying tables/attributeset.py -> build/lib.linux-aarch64-3.6/tables copying tables/exceptions.py -> build/lib.linux-aarch64-3.6/tables copying tables/table.py -> build/lib.linux-aarch64-3.6/tables copying tables/group.py -> build/lib.linux-aarch64-3.6/tables copying tables/expression.py -> build/lib.linux-aarch64-3.6/tables copying tables/unimplemented.py -> build/lib.linux-aarch64-3.6/tables copying tables/undoredo.py -> build/lib.linux-aarch64-3.6/tables copying tables/req_versions.py -> build/lib.linux-aarch64-3.6/tables copying tables/path.py -> build/lib.linux-aarch64-3.6/tables creating build/lib.linux-aarch64-3.6/tables/nodes copying tables/nodes/filenode.py -> build/lib.linux-aarch64-3.6/tables/nodes copying tables/nodes/init.py -> build/lib.linux-aarch64-3.6/tables/nodes creating build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_expression.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_indexvalues.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/create_backcompat_indexes.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_tablesMD.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/common.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_timestamps.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_do_undo.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_timetype.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_suite.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_enum.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_hdf5compat.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_carray.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_attributes.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_garbage.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_earray.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_basics.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_tables.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_indexes.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_aux.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_types.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/init.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_queries.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_array.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_utils.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_create.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_nestedtypes.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_lists.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_index_backcompat.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_backcompat.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_numpy.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_vlarray.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/check_leaks.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_tree.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_links.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_all.py -> build/lib.linux-aarch64-3.6/tables/tests creating build/lib.linux-aarch64-3.6/tables/misc copying tables/misc/proxydict.py -> build/lib.linux-aarch64-3.6/tables/misc copying tables/misc/enum.py -> build/lib.linux-aarch64-3.6/tables/misc copying tables/misc/init.py -> build/lib.linux-aarch64-3.6/tables/misc creating build/lib.linux-aarch64-3.6/tables/scripts copying tables/scripts/pttree.py -> build/lib.linux-aarch64-3.6/tables/scripts copying tables/scripts/ptrepack.py -> build/lib.linux-aarch64-3.6/tables/scripts copying tables/scripts/ptdump.py -> build/lib.linux-aarch64-3.6/tables/scripts copying tables/scripts/init.py -> build/lib.linux-aarch64-3.6/tables/scripts copying tables/scripts/pt2to3.py -> build/lib.linux-aarch64-3.6/tables/scripts creating build/lib.linux-aarch64-3.6/tables/nodes/tests copying tables/nodes/tests/test_filenode.py -> build/lib.linux-aarch64-3.6/tables/nodes/tests copying tables/nodes/tests/init.py -> build/lib.linux-aarch64-3.6/tables/nodes/tests copying tables/tests/itemsize.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/vlstr_attr.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/elink.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/bug-idx.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/idx-std-1.x.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/zerodim-attrs-1.3.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/indexes_2_0.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/ex-noattr.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/float.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_i64le.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_unsupptype.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/Tables_lzo1_shuffle.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/times-nested-be.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/Tables_lzo2.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_i32be.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/Tables_lzo2_shuffle.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/vlunicode_endian.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/blosc_bigendian.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/Table2_1_lzo_nrv2e_shuffle.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/issue_368.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/time-table-vlarray-1_x.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/nested-type-with-gaps.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_enum.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/python2.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/non-chunked-table.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/oldflavor_numeric.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_f64le.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/array_mdatom.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_f64be.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_szip.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/scalar.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/slink.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_SDSextendible.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_i64be.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/issue_560.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_compound_chunked.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/indexes_2_1.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/Tables_lzo1.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/flavored_vlarrays-format1.6.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_i32le.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/attr-u16.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/elink2.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/python3.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/zerodim-attrs-1.4.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_ref_array2.mat -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/matlab_file.mat -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_ref_array1.mat -> build/lib.linux-aarch64-3.6/tables/tests copying tables/nodes/tests/test_filenode.dat -> build/lib.linux-aarch64-3.6/tables/nodes/tests copying tables/nodes/tests/test_filenode.xbm -> build/lib.linux-aarch64-3.6/tables/nodes/tests copying tables/nodes/tests/test_filenode_v1.h5 -> build/lib.linux-aarch64-3.6/tables/nodes/tests running build_ext ---------------------------------------- ERROR: Command errored out with exit status -4: /home/dario/dlc-live/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-p9_amnr6/tables_db97b7244bac4c15a79f2d6898028816/setup.py'"'"'; file='"'"'/tmp/pip-install-p9_amnr6/tables_db97b7244bac4c15a79f2d6898028816/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-wtlkb57w/install-record.txt --single-version-externally-managed --compile --install-headers /home/dario/dlc-live/include/site/python3.6/tables Check the logs for full command output.

darioringach avatar Mar 15 '21 23:03 darioringach

I've had a heck of a time getting it to run on my Jetson as well. Once I finally got it up and running, I found that I couldn't get it to run CSI cameras because I couldn't figure out how to modify the opencv code. I'm just about done with everything Jetson-related. Seems like 10% of my time on them is actually normal function, and 90% endless tabs of stack exchange troubleshooting.

arge-7 avatar Mar 16 '21 00:03 arge-7

@arge-7 Yes, I feel your pain... and yet, the Jetson looks such a good fit for this it may be worth one more attempt.
Did you see this example? https://github.com/JetsonHacksNano/CSI-Camera

darioringach avatar Mar 16 '21 01:03 darioringach

Hmmm... maybe libhdf5-serial-dev is missing from the dependencies? I will try tomorrow.

darioringach avatar Mar 16 '21 03:03 darioringach

Also can you try installing directly from github: pip install git+https://github.com/DeepLabCut/DeepLabCut-live-GUI? There are some platform-specific dependencies, like PyTables, that I think aren't specified correctly for installing from PyPi. There has been a lot more testing of this install procedure locally/from github, so give it a shot and maybe it will ignore these issues with PyTables. And hopefully we can fix these issues with installing from PyPi soon :)

gkane26 avatar Mar 16 '21 14:03 gkane26

pip install git+https://github.com/DeepLabCut/DeepLabCut-live-GUI

Runs into --

Running setup.py install for tables ... error ERROR: Command errored out with exit status -4: command: /home/dario/dlc-live/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-aoqh93l7/tables_d01f396902fb44cbaa0a58ac73e4d5cd/setup.py'"'"'; file='"'"'/tmp/pip-install-aoqh93l7/tables_d01f396902fb44cbaa0a58ac73e4d5cd/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-ufjhl_tb/install-record.txt --single-version-externally-managed --compile --install-headers /home/dario/dlc-live/include/site/python3.6/tables cwd: /tmp/pip-install-aoqh93l7/tables_d01f396902fb44cbaa0a58ac73e4d5cd/ Complete output (188 lines): * Using Python 3.6.9 (default, Jan 26 2021, 15:33:00) * USE_PKGCONFIG: True * pkg-config header dirs for HDF5: /usr/include/hdf5/serial * pkg-config library dirs for HDF5: /usr/lib/aarch64-linux-gnu/hdf5/serial * Found HDF5 headers at /usr/include/hdf5/serial, library at /usr/lib/aarch64-linux-gnu/hdf5/serial. .. WARNING:: Could not find the HDF5 runtime. The HDF5 shared library was not found in the default library paths. In case of runtime problems, please remember to install it. /tmp/lzo_version_datetf0uunbz.c:1:1: warning: return type defaults to ‘int’ [-Wimplicit-int] main (int argc, char **argv) { ^~~~ /tmp/lzo_version_datetf0uunbz.c: In function ‘main’: /tmp/lzo_version_datetf0uunbz.c:2:5: warning: implicit declaration of function ‘lzo_version_date’ [-Wimplicit-function-declaration] lzo_version_date(); ^~~~~~~~~~~~~~~~ /usr/bin/ld: cannot find -llzo2 collect2: error: ld returned 1 exit status * Could not find LZO 2 headers and library; disabling support for it. /tmp/lzo_version_datebqvpdih1.c:1:1: warning: return type defaults to ‘int’ [-Wimplicit-int] main (int argc, char **argv) { ^~~~ /tmp/lzo_version_datebqvpdih1.c: In function ‘main’: /tmp/lzo_version_datebqvpdih1.c:2:5: warning: implicit declaration of function ‘lzo_version_date’ [-Wimplicit-function-declaration] lzo_version_date(); ^~~~~~~~~~~~~~~~ /usr/bin/ld: cannot find -llzo collect2: error: ld returned 1 exit status * Could not find LZO 1 headers and library; disabling support for it. /tmp/BZ2_bzlibVersionsc29z5_q.c:1:1: warning: return type defaults to ‘int’ [-Wimplicit-int] main (int argc, char **argv) { ^~~~ /tmp/BZ2_bzlibVersionsc29z5_q.c: In function ‘main’: /tmp/BZ2_bzlibVersionsc29z5_q.c:2:5: warning: implicit declaration of function ‘BZ2_bzlibVersion’ [-Wimplicit-function-declaration] BZ2_bzlibVersion(); ^~~~~~~~~~~~~~~~ /usr/bin/ld: cannot find -lbz2 collect2: error: ld returned 1 exit status * Could not find bzip2 headers and library; disabling support for it. /tmp/blosc_list_compressorsnjquiwlz.c:1:1: warning: return type defaults to ‘int’ [-Wimplicit-int] main (int argc, char **argv) { ^~~~ /tmp/blosc_list_compressorsnjquiwlz.c: In function ‘main’: /tmp/blosc_list_compressorsnjquiwlz.c:2:5: warning: implicit declaration of function ‘blosc_list_compressors’ [-Wimplicit-function-declaration] blosc_list_compressors(); ^~~~~~~~~~~~~~~~~~~~~~ /usr/bin/ld: cannot find -lblosc collect2: error: ld returned 1 exit status * Could not find blosc headers and library; using internal sources. /usr/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'extra_require' warnings.warn(msg) running install running build running build_py creating build creating build/lib.linux-aarch64-3.6 creating build/lib.linux-aarch64-3.6/tables copying tables/idxutils.py -> build/lib.linux-aarch64-3.6/tables copying tables/leaf.py -> build/lib.linux-aarch64-3.6/tables copying tables/vlarray.py -> build/lib.linux-aarch64-3.6/tables copying tables/node.py -> build/lib.linux-aarch64-3.6/tables copying tables/flavor.py -> build/lib.linux-aarch64-3.6/tables copying tables/filters.py -> build/lib.linux-aarch64-3.6/tables copying tables/carray.py -> build/lib.linux-aarch64-3.6/tables copying tables/atom.py -> build/lib.linux-aarch64-3.6/tables copying tables/conditions.py -> build/lib.linux-aarch64-3.6/tables copying tables/parameters.py -> build/lib.linux-aarch64-3.6/tables copying tables/utils.py -> build/lib.linux-aarch64-3.6/tables copying tables/file.py -> build/lib.linux-aarch64-3.6/tables copying tables/registry.py -> build/lib.linux-aarch64-3.6/tables copying tables/indexes.py -> build/lib.linux-aarch64-3.6/tables copying tables/link.py -> build/lib.linux-aarch64-3.6/tables copying tables/init.py -> build/lib.linux-aarch64-3.6/tables copying tables/index.py -> build/lib.linux-aarch64-3.6/tables copying tables/earray.py -> build/lib.linux-aarch64-3.6/tables copying tables/array.py -> build/lib.linux-aarch64-3.6/tables copying tables/description.py -> build/lib.linux-aarch64-3.6/tables copying tables/attributeset.py -> build/lib.linux-aarch64-3.6/tables copying tables/exceptions.py -> build/lib.linux-aarch64-3.6/tables copying tables/table.py -> build/lib.linux-aarch64-3.6/tables copying tables/group.py -> build/lib.linux-aarch64-3.6/tables copying tables/expression.py -> build/lib.linux-aarch64-3.6/tables copying tables/unimplemented.py -> build/lib.linux-aarch64-3.6/tables copying tables/undoredo.py -> build/lib.linux-aarch64-3.6/tables copying tables/req_versions.py -> build/lib.linux-aarch64-3.6/tables copying tables/path.py -> build/lib.linux-aarch64-3.6/tables creating build/lib.linux-aarch64-3.6/tables/nodes copying tables/nodes/filenode.py -> build/lib.linux-aarch64-3.6/tables/nodes copying tables/nodes/init.py -> build/lib.linux-aarch64-3.6/tables/nodes creating build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_expression.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_indexvalues.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/create_backcompat_indexes.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_tablesMD.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/common.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_timestamps.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_do_undo.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_timetype.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_suite.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_enum.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_hdf5compat.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_carray.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_attributes.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_garbage.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_earray.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_basics.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_tables.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_indexes.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_aux.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_types.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/init.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_queries.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_array.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_utils.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_create.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_nestedtypes.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_lists.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_index_backcompat.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_backcompat.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_numpy.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_vlarray.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/check_leaks.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_tree.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_links.py -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_all.py -> build/lib.linux-aarch64-3.6/tables/tests creating build/lib.linux-aarch64-3.6/tables/misc copying tables/misc/proxydict.py -> build/lib.linux-aarch64-3.6/tables/misc copying tables/misc/enum.py -> build/lib.linux-aarch64-3.6/tables/misc copying tables/misc/init.py -> build/lib.linux-aarch64-3.6/tables/misc creating build/lib.linux-aarch64-3.6/tables/scripts copying tables/scripts/pttree.py -> build/lib.linux-aarch64-3.6/tables/scripts copying tables/scripts/ptrepack.py -> build/lib.linux-aarch64-3.6/tables/scripts copying tables/scripts/ptdump.py -> build/lib.linux-aarch64-3.6/tables/scripts copying tables/scripts/init.py -> build/lib.linux-aarch64-3.6/tables/scripts copying tables/scripts/pt2to3.py -> build/lib.linux-aarch64-3.6/tables/scripts creating build/lib.linux-aarch64-3.6/tables/nodes/tests copying tables/nodes/tests/test_filenode.py -> build/lib.linux-aarch64-3.6/tables/nodes/tests copying tables/nodes/tests/init.py -> build/lib.linux-aarch64-3.6/tables/nodes/tests copying tables/tests/itemsize.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/vlstr_attr.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/elink.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/bug-idx.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/idx-std-1.x.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/zerodim-attrs-1.3.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/indexes_2_0.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/ex-noattr.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/float.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_i64le.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_unsupptype.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/Tables_lzo1_shuffle.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/times-nested-be.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/Tables_lzo2.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_i32be.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/Tables_lzo2_shuffle.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/vlunicode_endian.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/blosc_bigendian.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/Table2_1_lzo_nrv2e_shuffle.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/issue_368.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/time-table-vlarray-1_x.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/nested-type-with-gaps.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_enum.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/python2.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/non-chunked-table.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/oldflavor_numeric.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_f64le.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/array_mdatom.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_f64be.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_szip.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/scalar.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/slink.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_SDSextendible.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_i64be.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/issue_560.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_compound_chunked.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/indexes_2_1.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/Tables_lzo1.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/flavored_vlarrays-format1.6.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/smpl_i32le.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/attr-u16.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/elink2.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/python3.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/zerodim-attrs-1.4.h5 -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_ref_array2.mat -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/matlab_file.mat -> build/lib.linux-aarch64-3.6/tables/tests copying tables/tests/test_ref_array1.mat -> build/lib.linux-aarch64-3.6/tables/tests copying tables/nodes/tests/test_filenode.dat -> build/lib.linux-aarch64-3.6/tables/nodes/tests copying tables/nodes/tests/test_filenode.xbm -> build/lib.linux-aarch64-3.6/tables/nodes/tests copying tables/nodes/tests/test_filenode_v1.h5 -> build/lib.linux-aarch64-3.6/tables/nodes/tests running build_ext ---------------------------------------- ERROR: Command errored out with exit status -4: /home/dario/dlc-live/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-aoqh93l7/tables_d01f396902fb44cbaa0a58ac73e4d5cd/setup.py'"'"'; file='"'"'/tmp/pip-install-aoqh93l7/tables_d01f396902fb44cbaa0a58ac73e4d5cd/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-ufjhl_tb/install-record.txt --single-version-externally-managed --compile --install-headers /home/dario/dlc-live/include/site/python3.6/tables Check the logs for full command output.

darioringach avatar Mar 16 '21 14:03 darioringach

My bad -- tables is still a dependency for DeepLabCut-live-GUI on Jetson, but it shouldn't be for DeepLabCut-live. You could try to install just deeplabcut-live from github: pip install git+https://github.com/DeepLabCut-live, but you'll probably still run into this issue installing PyTables when installing the GUI package. hdf5 should have been installed in earlier steps according to [DeepLabCut-live Jetson install instructions] (https://github.com/DeepLabCut/DeepLabCut-live/blob/master/docs/install_jetson.md). Did these earlier steps complete successfully?

gkane26 avatar Mar 16 '21 15:03 gkane26

So does deeplabcut-live work for you? I remember that when I was having trouble getting the GUI version to run, I fixed it by doing a clean installation of live and then live GUI, mostly per the Github instructions except for some dependency annoyances.

arge-7 avatar Mar 16 '21 15:03 arge-7

Yes, earlier steps completed. It seems HDF5 gets installed in a non-standard location. Trying to see if I can fix with an environment variable (HDF5_DIR) pointing in the right direction.

darioringach avatar Mar 16 '21 15:03 darioringach

Ok... that seemed to fix tables -- but now it got stuck downloading multiple versions of pretty much everthing to determiine compatibility requirements....

INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime. If you want to abort this run, you can press Ctrl + C to do so. To improve how pip performs, tell us what happened here: https://pip.pypa.io/surveys/backtracking

darioringach avatar Mar 16 '21 15:03 darioringach

Oh well.... giving up on the Jetson for now. Happy to try again when installation kinks are worked out. @arge-7 did it work for you at least with USB cameras?

darioringach avatar Mar 16 '21 15:03 darioringach

I actually never tried that because I needed to use specific raspberry pi IR cameras for my use case. I did get dlcllive and dlclivegui up and running eventually though. Just never got to use a camera with it. I may come back to trying to get the CSI cameras to work because I think I've found some code that will fix the problem.

arge-7 avatar Mar 16 '21 15:03 arge-7

HI all, be sure you are using python 3.6 not 3.8 btw!

MMathisLab avatar Mar 16 '21 15:03 MMathisLab

I'm using 3.6.9

darioringach avatar Mar 16 '21 15:03 darioringach

Yoohoo... It worked! But it didn't install the check_install --

(dlc-live) dario@dario-jetson:~$ dlc-live-test 
Traceback (most recent call last):
  File "/home/dario/dlc-live/bin/dlc-live-test", line 5, in <module>
    from check_install.check_install import main
ModuleNotFoundError: No module named 'check_install'

Did I skip something?

darioringach avatar Mar 16 '21 20:03 darioringach

Will a model developed with tensorflow 1.13.1 run with DLC Live and tensorflow 1.15.4?
Or is the incompatibility just between 1 and 2?

darioringach avatar Mar 16 '21 21:03 darioringach

It generally should be the exact same, it’s not just 1 v 2 sadly

MMathisLab avatar Mar 16 '21 21:03 MMathisLab