Please read this post, not the previous one (Installation errors)

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Sasha G

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Mar 28, 2022, 2:25:05 PM3/28/22

to majiq_voila

Hello,

I managed to find the right paths for gcc/g++ but I am still getting an error message.

Best,

Sasha

(base) Sashas-MacBook-Pro-2:bin sasha$ export HTSLIB_LIBRARY_DIR=/Users/sasha/Downloads/HTS/lib

(base) Sashas-MacBook-Pro-2:bin sasha$ export HTSLIB_INCLUDE_DIR=/Users/sasha/Downloads/HTS/include

(base) Sashas-MacBook-Pro-2:bin sasha$ export CC=/usr/local/bin/gcc-11

(base) Sashas-MacBook-Pro-2:bin sasha$ export CXX=/usr/local/bin/g++-11

(base) Sashas-MacBook-Pro-2:bin sasha$ pip install git+https://bitbucket.org/biociphers/majiq_academic.git

Collecting git+https://bitbucket.org/biociphers/majiq_academic.git

Cloning https://bitbucket.org/biociphers/majiq_academic.git to /private/var/folders/_6/w95_jy1x1n14fq8fjx7cnncc0000gn/T/pip-req-build-43gf4xh4

Running command git clone --filter=blob:none --quiet https://bitbucket.org/biociphers/majiq_academic.git /private/var/folders/_6/w95_jy1x1n14fq8fjx7cnncc0000gn/T/pip-req-build-43gf4xh4

warning: filtering not recognized by server, ignoring

Resolved https://bitbucket.org/biociphers/majiq_academic.git to commit 85d07819f55b182c830bdc69296c1485f51b3100

Installing build dependencies ... done

Getting requirements to build wheel ... done

Preparing metadata (pyproject.toml) ... done

Processing /private/var/folders/_6/w95_jy1x1n14fq8fjx7cnncc0000gn/T/pip-req-build-43gf4xh4/majiq

Installing build dependencies ... done

Getting requirements to build wheel ... done

Preparing metadata (pyproject.toml) ... done

Processing /private/var/folders/_6/w95_jy1x1n14fq8fjx7cnncc0000gn/T/pip-req-build-43gf4xh4/voila

Installing build dependencies ... done

Getting requirements to build wheel ... done

Preparing metadata (pyproject.toml) ... done

Collecting scipy>=1.4.1

Using cached scipy-1.8.0-cp39-cp39-macosx_12_0_universal2.macosx_10_9_x86_64.whl (55.6 MB)

Collecting smmap2==2.0.5

Using cached smmap2-2.0.5-py2.py3-none-any.whl (24 kB)

Collecting numpy>=1.18.1

Using cached numpy-1.22.3-cp39-cp39-macosx_10_14_x86_64.whl (17.6 MB)

Collecting Jinja2==2.11.1

Using cached Jinja2-2.11.1-py2.py3-none-any.whl (126 kB)

Collecting psutil==5.6.7

Using cached psutil-5.6.7-cp39-cp39-macosx_10_9_x86_64.whl

Collecting gitdb2==2.0.6

Using cached gitdb2-2.0.6-py2.py3-none-any.whl (63 kB)

Collecting Flask-WTF==0.14.2

Using cached Flask_WTF-0.14.2-py2.py3-none-any.whl (14 kB)

Collecting Werkzeug==0.16.0

Using cached Werkzeug-0.16.0-py2.py3-none-any.whl (327 kB)

Collecting WTForms==2.2.1

Using cached WTForms-2.2.1-py2.py3-none-any.whl (166 kB)

Collecting Click>=7.0

Using cached click-8.1.0-py3-none-any.whl (96 kB)

Collecting waitress==1.1.0

Using cached waitress-1.1.0-py2.py3-none-any.whl (114 kB)

Collecting MarkupSafe==1.1.1

Using cached MarkupSafe-1.1.1-cp39-cp39-macosx_10_9_x86_64.whl (16 kB)

Collecting Flask==1.0.2

Using cached Flask-1.0.2-py2.py3-none-any.whl (91 kB)

Collecting GitPython==3.0.5

Using cached GitPython-3.0.5-py3-none-any.whl (455 kB)

Collecting networkx==2.5

Using cached networkx-2.5-py3-none-any.whl (1.6 MB)

Collecting Flask-Session==0.3.1

Using cached Flask_Session-0.3.1-py2.py3-none-any.whl (7.5 kB)

Collecting itsdangerous==1.1.0

Using cached itsdangerous-1.1.0-py2.py3-none-any.whl (16 kB)

Collecting gunicorn==19.9.0

Using cached gunicorn-19.9.0-py2.py3-none-any.whl (112 kB)

Collecting h5py==2.10.0

Using cached h5py-2.10.0.tar.gz (301 kB)

Preparing metadata (setup.py) ... done

Collecting six==1.14.0

Using cached six-1.14.0-py2.py3-none-any.whl (10 kB)

Collecting decorator>=4.3.0

Using cached decorator-5.1.1-py3-none-any.whl (9.1 kB)

Using legacy 'setup.py install' for h5py, since package 'wheel' is not installed.

Building wheels for collected packages: rna-majiq-meta, rna-majiq, rna-voila

Building wheel for rna-majiq-meta (pyproject.toml) ... done

Created wheel for rna-majiq-meta: filename=rna_majiq_meta-2.4.dev3+g85d07819-py3-none-any.whl size=1404 sha256=37f8da965959c16a0f80de0791b8273a8156c9cffd735bad5ee3405eccaa69c4

Stored in directory: /private/var/folders/_6/w95_jy1x1n14fq8fjx7cnncc0000gn/T/pip-ephem-wheel-cache-bopaiko4/wheels/65/a2/b4/cf0224fa47e5625c1254d988698fc75cba73527e06d433e201

Building wheel for rna-majiq (pyproject.toml) ... done

Created wheel for rna-majiq: filename=rna_majiq-2.4.dev3+g85d07819-cp39-cp39-macosx_10_9_x86_64.whl size=6834565 sha256=13e809c3f8acab9b9921d96fefe00751082e626b70fff9abc6783fd20d19ad08

Stored in directory: /private/var/folders/_6/w95_jy1x1n14fq8fjx7cnncc0000gn/T/pip-ephem-wheel-cache-bopaiko4/wheels/95/ae/88/487e67b4663426c9a65137d61bd9fef848497c43a28ce910d0

Building wheel for rna-voila (pyproject.toml) ... done

Created wheel for rna-voila: filename=rna_voila-2.4.dev3+g85d07819-py3-none-any.whl size=2451745 sha256=212f6f875d1d02250871515a0c65dc536d74f4c0fcfd7b85dbe3c531fc512617

Stored in directory: /private/var/folders/_6/w95_jy1x1n14fq8fjx7cnncc0000gn/T/pip-ephem-wheel-cache-bopaiko4/wheels/4f/6b/35/33f6d077537c0ebd6ad7857dd2182bf9ae6a874f682e662a9a

Successfully built rna-majiq-meta rna-majiq rna-voila

Installing collected packages: WTForms, waitress, Werkzeug, smmap2, six, psutil, numpy, MarkupSafe, itsdangerous, gunicorn, decorator, Click, scipy, networkx, Jinja2, h5py, gitdb2, GitPython, Flask, Flask-WTF, Flask-Session, rna-voila, rna-majiq, rna-majiq-meta

Running setup.py install for h5py ... error

error: subprocess-exited-with-error

× Running setup.py install for h5py did not run successfully.

│ exit code: 1

╰─> [1453 lines of output]

WARNING: The wheel package is not available.

running install

running build

running build_py

creating build

creating build/lib.macosx-10.9-x86_64-3.9

creating build/lib.macosx-10.9-x86_64-3.9/h5py

copying h5py/h5py_warnings.py -> build/lib.macosx-10.9-x86_64-3.9/h5py

copying h5py/version.py -> build/lib.macosx-10.9-x86_64-3.9/h5py

copying h5py/highlevel.py -> build/lib.macosx-10.9-x86_64-3.9/h5py

copying h5py/__init__.py -> build/lib.macosx-10.9-x86_64-3.9/h5py

copying h5py/ipy_completer.py -> build/lib.macosx-10.9-x86_64-3.9/h5py

creating build/lib.macosx-10.9-x86_64-3.9/h5py/_hl

copying h5py/_hl/files.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/_hl

copying h5py/_hl/compat.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/_hl

copying h5py/_hl/__init__.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/_hl

copying h5py/_hl/selections.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/_hl

copying h5py/_hl/dataset.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/_hl

copying h5py/_hl/vds.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/_hl

copying h5py/_hl/selections2.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/_hl

copying h5py/_hl/group.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/_hl

copying h5py/_hl/datatype.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/_hl

copying h5py/_hl/attrs.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/_hl

copying h5py/_hl/dims.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/_hl

copying h5py/_hl/base.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/_hl

copying h5py/_hl/filters.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/_hl

creating build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_deprecation.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_dimension_scales.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_attribute_create.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_file_image.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_h5f.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_dataset_getitem.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_group.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_dataset_swmr.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_slicing.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_h5pl.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_attrs.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_attrs_data.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_h5t.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_h5p.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_datatype.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/common.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_dataset.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_file.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_selections.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_threads.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_dtype.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_h5.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_file2.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_completions.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_filters.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_base.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

copying h5py/tests/test_objects.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests

creating build/lib.macosx-10.9-x86_64-3.9/h5py/tests/test_vds

copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests/test_vds

copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests/test_vds

copying h5py/tests/test_vds/__init__.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests/test_vds

copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.macosx-10.9-x86_64-3.9/h5py/tests/test_vds

running build_ext

Loading library to get version: /usr/local/lib/libhdf5.dylib

Autodetected HDF5 1.13.0

********************************************************************************

Summary of the h5py configuration

Path to HDF5: None

HDF5 Version: '1.13.0'

MPI Enabled: False

Rebuild Required: True

********************************************************************************

Executing api_gen rebuild of defs

Executing cythonize()

[ 1/23] Cythonizing /private/var/folders/_6/w95_jy1x1n14fq8fjx7cnncc0000gn/T/pip-install-gb0u8cw7/h5py_38935838ccb74e4081d315669cfec623/h5py/_conv.pyx

warning: h5py/api_types_hdf5.pxd:418:2: 'H5D_layout_t' redeclared

warning: h5py/api_types_hdf5.pxd:425:2: 'H5D_alloc_time_t' redeclared

warning: h5py/api_types_hdf5.pxd:432:2: 'H5D_space_status_t' redeclared

warning: h5py/api_types_hdf5.pxd:438:2: 'H5D_fill_time_t' redeclared

warning: h5py/api_types_hdf5.pxd:444:2: 'H5D_fill_value_t' redeclared

warning: h5py/api_types_hdf5.pxd:456:7: 'H5F_close_degree_t' redeclared

warning: h5py/api_types_hdf5.pxd:462:2: 'H5FD_mem_t' redeclared

warning: h5py/api_types_hdf5.pxd:560:2: 'H5T_cset_t' redeclared

warning: h5py/api_types_hdf5.pxd:739:7: 'H5Z_EDC_t' redeclared

warning: h5py/api_types_hdf5.pxd:419:4: 'H5D_LAYOUT_ERROR' redeclared

warning: h5py/api_types_hdf5.pxd:420:4: 'H5D_COMPACT' redeclared

warning: h5py/api_types_hdf5.pxd:421:4: 'H5D_CONTIGUOUS' redeclared

warning: h5py/api_types_hdf5.pxd:422:4: 'H5D_CHUNKED' redeclared

warning: h5py/api_types_hdf5.pxd:423:4: 'H5D_NLAYOUTS' redeclared

warning: h5py/api_types_hdf5.pxd:426:4: 'H5D_ALLOC_TIME_ERROR' redeclared

warning: h5py/api_types_hdf5.pxd:427:4: 'H5D_ALLOC_TIME_DEFAULT' redeclared

warning: h5py/api_types_hdf5.pxd:428:4: 'H5D_ALLOC_TIME_EARLY' redeclared

warning: h5py/api_types_hdf5.pxd:429:4: 'H5D_ALLOC_TIME_LATE' redeclared

warning: h5py/api_types_hdf5.pxd:430:4: 'H5D_ALLOC_TIME_INCR' redeclared

warning: h5py/api_types_hdf5.pxd:433:4: 'H5D_SPACE_STATUS_ERROR' redeclared

warning: h5py/api_types_hdf5.pxd:434:4: 'H5D_SPACE_STATUS_NOT_ALLOCATED' redeclared

warning: h5py/api_types_hdf5.pxd:435:4: 'H5D_SPACE_STATUS_PART_ALLOCATED' redeclared

warning: h5py/api_types_hdf5.pxd:436:4: 'H5D_SPACE_STATUS_ALLOCATED' redeclared

warning: h5py/api_types_hdf5.pxd:439:4: 'H5D_FILL_TIME_ERROR' redeclared

warning: h5py/api_types_hdf5.pxd:440:4: 'H5D_FILL_TIME_ALLOC' redeclared

warning: h5py/api_types_hdf5.pxd:441:4: 'H5D_FILL_TIME_NEVER' redeclared

warning: h5py/api_types_hdf5.pxd:442:4: 'H5D_FILL_TIME_IFSET' redeclared

warning: h5py/api_types_hdf5.pxd:445:4: 'H5D_FILL_VALUE_ERROR' redeclared

warning: h5py/api_types_hdf5.pxd:446:4: 'H5D_FILL_VALUE_UNDEFINED' redeclared

warning: h5py/api_types_hdf5.pxd:447:4: 'H5D_FILL_VALUE_DEFAULT' redeclared

warning: h5py/api_types_hdf5.pxd:448:4: 'H5D_FILL_VALUE_USER_DEFINED' redeclared

warning: h5py/api_types_hdf5.pxd:457:4: 'H5F_CLOSE_WEAK' redeclared

warning: h5py/api_types_hdf5.pxd:458:4: 'H5F_CLOSE_SEMI' redeclared

warning: h5py/api_types_hdf5.pxd:459:4: 'H5F_CLOSE_STRONG' redeclared

warning: h5py/api_types_hdf5.pxd:460:4: 'H5F_CLOSE_DEFAULT' redeclared

warning: h5py/api_types_hdf5.pxd:463:4: 'H5FD_MEM_NOLIST' redeclared

warning: h5py/api_types_hdf5.pxd:464:4: 'H5FD_MEM_DEFAULT' redeclared

warning: h5py/api_types_hdf5.pxd:465:4: 'H5FD_MEM_SUPER' redeclared

warning: h5py/api_types_hdf5.pxd:466:4: 'H5FD_MEM_BTREE' redeclared

warning: h5py/api_types_hdf5.pxd:467:4: 'H5FD_MEM_DRAW' redeclared

warning: h5py/api_types_hdf5.pxd:468:4: 'H5FD_MEM_GHEAP' redeclared

warning: h5py/api_types_hdf5.pxd:469:4: 'H5FD_MEM_LHEAP' redeclared

warning: h5py/api_types_hdf5.pxd:470:4: 'H5FD_MEM_OHDR' redeclared

warning: h5py/api_types_hdf5.pxd:471:4: 'H5FD_MEM_NTYPES' redeclared

warning: h5py/api_types_hdf5.pxd:561:4: 'H5T_CSET_ERROR' redeclared

warning: h5py/api_types_hdf5.pxd:562:4: 'H5T_CSET_ASCII' redeclared

warning: h5py/api_types_hdf5.pxd:705:2: 'H5Z_filter_t' redeclared

warning: h5py/api_types_hdf5.pxd:740:6: 'H5Z_ERROR_EDC' redeclared

warning: h5py/api_types_hdf5.pxd:741:6: 'H5Z_DISABLE_EDC' redeclared

warning: h5py/api_types_hdf5.pxd:742:6: 'H5Z_ENABLE_EDC' redeclared

warning: h5py/api_types_hdf5.pxd:743:6: 'H5Z_NO_EDC' redeclared

[ 2/23] Cythonizing /private/var/folders/_6/w95_jy1x1n14fq8fjx7cnncc0000gn/T/pip-install-gb0u8cw7/h5py_38935838ccb74e4081d315669cfec623/h5py/_errors.pyx