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hoffmangroup / genomedata

The Genomedata format for storing large-scale functional genomics data.
https://genomedata.hoffmanlab.org/
GNU General Public License v2.0
2 stars 1 forks source link

`pip install genomedata` attempts to find /usr/bin/gcc-4.0 which may not exist #45

Closed EricR86 closed 6 years ago

EricR86 commented 6 years ago

Original report (archived issue) by Rachel Chan (Bitbucket: rcwchan).

I received an error while trying to install genomedata using pip (for python 3.7.0). To me it seems like it is trying to call on /usr/bin/gcc-4.0, which doesn't exist:

#!python

(genomedatatest) rachelc@mhoffman8: ~$ ll /usr/bin/ | grep gcc
lrwxrwxrwx    1 root root           3 Jan 22  2018 cc -> gcc
-rwxr-xr-x    2 root root      768592 Nov 30  2017 gcc
-rwxr-xr-x.   1 root root      266120 Jun  9  2014 gcc44
-rwxr-xr-x    1 root root       27088 Nov 30  2017 gcc-ar
-rwxr-xr-x.   1 root root        2046 Jun 10  2014 gccmakedep
-rwxr-xr-x    1 root root       27088 Nov 30  2017 gcc-nm
-rwxr-xr-x    1 root root       27088 Nov 30  2017 gcc-ranlib
lrwxrwxrwx    1 root root           3 Jan 22  2018 gnatgcc -> gcc
-rwxr-xr-x    2 root root      768592 Nov 30  2017 x86_64-redhat-linux-gcc

It also seems unable to find the hdf5 installed by conda:

#!python

  Package hdf5 was not found in the pkg-config search path.
  Perhaps you should add the directory containing `hdf5.pc'
  to the PKG_CONFIG_PATH environment variable
  No package 'hdf5' found

Below, I have reproduced the error using a fresh conda environment:

#!python

rachelc@mhoffman8: ~$ conda create --name genomedatatest
Solving environment: done

## Package Plan ##

  environment location: /scratch/miniconda3/envs/genomedatatest

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate genomedatatest
#
# To deactivate an active environment, use
#
#     $ conda deactivate

rachelc@mhoffman8: ~$ conda activate genomedatatest
(genomedatatest) rachelc@mhoffman8: ~$ conda install hdf5
Solving environment: done

## Package Plan ##

  environment location: /scratch/miniconda3/envs/genomedatatest

  added / updated specs: 
    - hdf5

The following NEW packages will be INSTALLED:

    hdf5:           1.10.2-hba1933b_1
    libgcc-ng:      8.2.0-hdf63c60_1 
    libgfortran-ng: 7.3.0-hdf63c60_0 
    libstdcxx-ng:   8.2.0-hdf63c60_1 
    zlib:           1.2.11-ha838bed_2

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(genomedatatest) rachelc@mhoffman8: ~$ pip install genomedata
Collecting genomedata
  Using cached https://files.pythonhosted.org/packages/ae/a8/095d15019a28d370b0f81a5adb289828dee17b5ac5e069518024526996f6/genomedata-1.4.4.tar.gz
Requirement already satisfied: numpy in /scratch/miniconda3/lib/python3.7/site-packages (from genomedata) (1.15.1)
Collecting tables!=3.4.1,>=3.0 (from genomedata)
  Downloading https://files.pythonhosted.org/packages/4d/53/8f34ce887c2a2ad80518980419a5f6f41defc85a287a355987e559ce9385/tables-3.4.4.tar.gz (4.6MB)
    100% |████████████████████████████████| 4.6MB 9.6MB/s 
Requirement already satisfied: six in /scratch/miniconda3/lib/python3.7/site-packages (from genomedata) (1.11.0)
Collecting textinput>=0.2.0 (from genomedata)
  Using cached https://files.pythonhosted.org/packages/f5/38/4bd1617eabd04154b465d6ce4b94e2f47b8168bc1ac7a33c437000bbb3bf/textinput-0.2.0.tar.gz
Collecting path.py>=11 (from genomedata)
  Using cached https://files.pythonhosted.org/packages/1c/56/123eb7d3d43af264f2cf0cfd995787fb9eed7531d6cf6622c9b78d51d933/path.py-11.4.1-py2.py3-none-any.whl
Collecting numexpr>=2.5.2 (from tables!=3.4.1,>=3.0->genomedata)
  Downloading https://files.pythonhosted.org/packages/d1/18/fc1611fd06e83c04e680e1f99060f9c2073a3b34286a87b917f0c025729b/numexpr-2.6.8-cp37-cp37m-manylinux1_x86_64.whl (163kB)
    100% |████████████████████████████████| 163kB 7.0MB/s 
Collecting importlib-metadata>=0.5 (from path.py>=11->genomedata)
  Using cached https://files.pythonhosted.org/packages/2a/d2/cbdcb1b718d7066512ebeb84f796c7e8d4a6b89f97e7346e792820521a62/importlib_metadata-0.5-py2.py3-none-any.whl
Building wheels for collected packages: genomedata, tables, textinput
  Running setup.py bdist_wheel for genomedata ... error
  Complete output from command /scratch/miniconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-ms2r486i/genomedata/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/pip-wheel-uk94oz9v --python-tag cp37:
  Package hdf5 was not found in the pkg-config search path.
  Perhaps you should add the directory containing `hdf5.pc'
  to the PKG_CONFIG_PATH environment variable
  No package 'hdf5' found
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib
  creating build/lib/genomedata
  copying genomedata/_util.py -> build/lib/genomedata
  copying genomedata/_erase_data.py -> build/lib/genomedata
  copying genomedata/_histogram.py -> build/lib/genomedata
  copying genomedata/_query.py -> build/lib/genomedata
  copying genomedata/load_genomedata.py -> build/lib/genomedata
  copying genomedata/_hardmask.py -> build/lib/genomedata
  copying genomedata/_info.py -> build/lib/genomedata
  copying genomedata/_load_seq.py -> build/lib/genomedata
  copying genomedata/_open_data.py -> build/lib/genomedata
  copying genomedata/_hardmask_parsers.py -> build/lib/genomedata
  copying genomedata/_load_data.py -> build/lib/genomedata
  copying genomedata/_report.py -> build/lib/genomedata
  copying genomedata/_close_data.py -> build/lib/genomedata
  copying genomedata/__init__.py -> build/lib/genomedata
  running egg_info
  writing genomedata.egg-info/PKG-INFO
  writing dependency_links to genomedata.egg-info/dependency_links.txt
  writing entry points to genomedata.egg-info/entry_points.txt
  writing requirements to genomedata.egg-info/requires.txt
  writing top-level names to genomedata.egg-info/top_level.txt
  reading manifest file 'genomedata.egg-info/SOURCES.txt'
  writing manifest file 'genomedata.egg-info/SOURCES.txt'
  running build_scripts
  ##################################################
  creating build/scripts-3.7
  creating build/scripts-3.7/Linux_x86_64
  creating build/scripts-3.7/Linux_x86_64/src
  /usr/bin/gcc-4.0 -Wsign-compare -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c src/genomedata_load_data.c -o build/scripts-3.7/Linux_x86_64/src/genomedata_load_data.o -std=c99 -pedantic -Wextra -Wno-missing-field-initializers -DH5_NO_DEPRECATED_SYMBOLS
  unable to execute '/usr/bin/gcc-4.0': No such file or directory
  error: command '/usr/bin/gcc-4.0' failed with exit status 1

  ----------------------------------------
  Failed building wheel for genomedata
  Running setup.py clean for genomedata
  Running setup.py bdist_wheel for tables ... error
  Complete output from command /scratch/miniconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-ms2r486i/tables/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/pip-wheel-ri6iq09u --python-tag cp37:
  * Using Python 3.7.0 (default, Jun 28 2018, 13:15:42)
  * USE_PKGCONFIG: True
  * Found conda env: ``/scratch/miniconda3/envs/genomedatatest``
  * Found HDF5 headers at ``/scratch/miniconda3/envs/genomedatatest/include``, library at ``/scratch/miniconda3/envs/genomedatatest/lib``.
  /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.
  /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.
  * Could not find bzip2 headers and library; disabling support for it.
  * Could not find blosc headers and library; using internal sources.
  SSE2 detected
  /scratch/miniconda3/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'extra_require'
    warnings.warn(msg)
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.7
  creating build/lib.linux-x86_64-3.7/tables
  copying tables/table.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/exceptions.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/undoredo.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/unimplemented.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/file.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/registry.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/attributeset.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/node.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/earray.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/parameters.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/link.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/filters.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/carray.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/indexes.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/index.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/req_versions.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/utils.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/expression.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/atom.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/group.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/array.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/conditions.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/vlarray.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/leaf.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/flavor.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/description.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/idxutils.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/__init__.py -> build/lib.linux-x86_64-3.7/tables
  copying tables/path.py -> build/lib.linux-x86_64-3.7/tables
  creating build/lib.linux-x86_64-3.7/tables/scripts
  copying tables/scripts/pt2to3.py -> build/lib.linux-x86_64-3.7/tables/scripts
  copying tables/scripts/pttree.py -> build/lib.linux-x86_64-3.7/tables/scripts
  copying tables/scripts/ptrepack.py -> build/lib.linux-x86_64-3.7/tables/scripts
  copying tables/scripts/ptdump.py -> build/lib.linux-x86_64-3.7/tables/scripts
  copying tables/scripts/__init__.py -> build/lib.linux-x86_64-3.7/tables/scripts
  creating build/lib.linux-x86_64-3.7/tables/nodes
  copying tables/nodes/filenode.py -> build/lib.linux-x86_64-3.7/tables/nodes
  copying tables/nodes/__init__.py -> build/lib.linux-x86_64-3.7/tables/nodes
  creating build/lib.linux-x86_64-3.7/tables/misc
  copying tables/misc/proxydict.py -> build/lib.linux-x86_64-3.7/tables/misc
  copying tables/misc/enum.py -> build/lib.linux-x86_64-3.7/tables/misc
  copying tables/misc/__init__.py -> build/lib.linux-x86_64-3.7/tables/misc
  creating build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_indexes.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_indexvalues.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_carray.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_hdf5compat.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_index_backcompat.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_attributes.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_utils.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/common.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_basics.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_all.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_lists.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_enum.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_garbage.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_vlarray.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_tables.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_aux.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_array.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/create_backcompat_indexes.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_links.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_queries.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_types.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_tree.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_nestedtypes.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/check_leaks.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_tablesMD.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_numpy.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_backcompat.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_do_undo.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_earray.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_create.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_timetype.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_timestamps.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/__init__.py -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_expression.py -> build/lib.linux-x86_64-3.7/tables/tests
  creating build/lib.linux-x86_64-3.7/tables/nodes/tests
  copying tables/nodes/tests/test_filenode.py -> build/lib.linux-x86_64-3.7/tables/nodes/tests
  copying tables/nodes/tests/__init__.py -> build/lib.linux-x86_64-3.7/tables/nodes/tests
  copying tables/tests/smpl_compound_chunked.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/blosc_bigendian.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/oldflavor_numeric.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/non-chunked-table.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/bug-idx.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/indexes_2_0.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/issue_368.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/python2.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/python3.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/Tables_lzo1_shuffle.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/smpl_f64be.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/array_mdatom.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/float.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/scalar.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/zerodim-attrs-1.4.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/smpl_i32le.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/flavored_vlarrays-format1.6.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/nested-type-with-gaps.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/vlunicode_endian.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/issue_560.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/attr-u16.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/smpl_i32be.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/zerodim-attrs-1.3.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/smpl_enum.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/elink.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/smpl_f64le.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/smpl_SDSextendible.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/Tables_lzo2.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/idx-std-1.x.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/times-nested-be.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/Tables_lzo2_shuffle.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/Table2_1_lzo_nrv2e_shuffle.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/smpl_i64le.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/time-table-vlarray-1_x.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/smpl_i64be.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/slink.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/elink2.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/ex-noattr.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/Tables_lzo1.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/vlstr_attr.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/smpl_unsupptype.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_szip.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/indexes_2_1.h5 -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_ref_array1.mat -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/matlab_file.mat -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/tests/test_ref_array2.mat -> build/lib.linux-x86_64-3.7/tables/tests
  copying tables/nodes/tests/test_filenode.dat -> build/lib.linux-x86_64-3.7/tables/nodes/tests
  copying tables/nodes/tests/test_filenode.xbm -> build/lib.linux-x86_64-3.7/tables/nodes/tests
  copying tables/nodes/tests/test_filenode_v1.h5 -> build/lib.linux-x86_64-3.7/tables/nodes/tests
  running build_ext
  building 'tables.utilsextension' extension
  creating build/temp.linux-x86_64-3.7
  creating build/temp.linux-x86_64-3.7/tables
  creating build/temp.linux-x86_64-3.7/src
  creating build/temp.linux-x86_64-3.7/hdf5-blosc
  creating build/temp.linux-x86_64-3.7/hdf5-blosc/src
  creating build/temp.linux-x86_64-3.7/c-blosc
  creating build/temp.linux-x86_64-3.7/c-blosc/blosc
  creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs
  creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/lz4-1.8.1.2
  creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/snappy-1.1.1
  creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zlib-1.2.8
  creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4
  creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/common
  creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/decompress
  creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/compress
  creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/legacy
  creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/deprecated
  creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/dictBuilder
  /usr/bin/gcc-4.0 -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DNDEBUG=1 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ihdf5-blosc/src -I/scratch/miniconda3/envs/genomedatatest/include -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.8.1.2 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.3.4 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.3.4/common -Ic-blosc/internal-complibs/zstd-1.3.4 -I/scratch/miniconda3/lib/python3.7/site-packages/numpy/core/include -I/scratch/miniconda3/include/python3.7m -c tables/utilsextension.c -o build/temp.linux-x86_64-3.7/tables/utilsextension.o -Isrc -DH5_USE_18_API -DH5Acreate_vers=2 -DH5Aiterate_vers=2 -DH5Dcreate_vers=2 -DH5Dopen_vers=2 -DH5Eclear_vers=2 -DH5Eprint_vers=2 -DH5Epush_vers=2 -DH5Eset_auto_vers=2 -DH5Eget_auto_vers=2 -DH5Ewalk_vers=2 -DH5E_auto_t_vers=2 -DH5Gcreate_vers=2 -DH5Gopen_vers=2 -DH5Pget_filter_vers=2 -DH5Pget_filter_by_id_vers=2 -DH5Tarray_create_vers=2 -DH5Tget_array_dims_vers=2 -DH5Z_class_t_vers=2 -DSHUFFLE_SSE2_ENABLED -msse2
  unable to execute '/usr/bin/gcc-4.0': No such file or directory
  error: command '/usr/bin/gcc-4.0' failed with exit status 1

  ----------------------------------------
  Failed building wheel for tables
  Running setup.py clean for tables
  Running setup.py bdist_wheel for textinput ... done
  Stored in directory: /users/rachelc/.cache/pip/wheels/22/a5/fa/49b6cabb4ebd585cea1796348431d0c89bcb6f48a69620b66c
Successfully built textinput
Failed to build genomedata tables
Installing collected packages: numexpr, tables, textinput, importlib-metadata, path.py, genomedata
  Running setup.py install for tables ... error
    Complete output from command /scratch/miniconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-ms2r486i/tables/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-ognnh04e/install-record.txt --single-version-externally-managed --compile:
    * Using Python 3.7.0 (default, Jun 28 2018, 13:15:42)
    * USE_PKGCONFIG: True
    * Found conda env: ``/scratch/miniconda3/envs/genomedatatest``
    * Found HDF5 headers at ``/scratch/miniconda3/envs/genomedatatest/include``, library at ``/scratch/miniconda3/envs/genomedatatest/lib``.
    /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.
    /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.
    * Could not find bzip2 headers and library; disabling support for it.
    * Could not find blosc headers and library; using internal sources.
    SSE2 detected
    /scratch/miniconda3/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'extra_require'
      warnings.warn(msg)
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.7
    creating build/lib.linux-x86_64-3.7/tables
    copying tables/table.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/exceptions.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/undoredo.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/unimplemented.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/file.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/registry.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/attributeset.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/node.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/earray.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/parameters.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/link.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/filters.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/carray.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/indexes.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/index.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/req_versions.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/utils.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/expression.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/atom.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/group.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/array.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/conditions.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/vlarray.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/leaf.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/flavor.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/description.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/idxutils.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/__init__.py -> build/lib.linux-x86_64-3.7/tables
    copying tables/path.py -> build/lib.linux-x86_64-3.7/tables
    creating build/lib.linux-x86_64-3.7/tables/scripts
    copying tables/scripts/pt2to3.py -> build/lib.linux-x86_64-3.7/tables/scripts
    copying tables/scripts/pttree.py -> build/lib.linux-x86_64-3.7/tables/scripts
    copying tables/scripts/ptrepack.py -> build/lib.linux-x86_64-3.7/tables/scripts
    copying tables/scripts/ptdump.py -> build/lib.linux-x86_64-3.7/tables/scripts
    copying tables/scripts/__init__.py -> build/lib.linux-x86_64-3.7/tables/scripts
    creating build/lib.linux-x86_64-3.7/tables/nodes
    copying tables/nodes/filenode.py -> build/lib.linux-x86_64-3.7/tables/nodes
    copying tables/nodes/__init__.py -> build/lib.linux-x86_64-3.7/tables/nodes
    creating build/lib.linux-x86_64-3.7/tables/misc
    copying tables/misc/proxydict.py -> build/lib.linux-x86_64-3.7/tables/misc
    copying tables/misc/enum.py -> build/lib.linux-x86_64-3.7/tables/misc
    copying tables/misc/__init__.py -> build/lib.linux-x86_64-3.7/tables/misc
    creating build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_indexes.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_indexvalues.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_carray.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_hdf5compat.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_index_backcompat.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_attributes.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_utils.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/common.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_basics.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_all.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_lists.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_enum.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_garbage.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_vlarray.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_tables.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_aux.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_array.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/create_backcompat_indexes.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_links.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_queries.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_types.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_tree.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_nestedtypes.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/check_leaks.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_tablesMD.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_numpy.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_backcompat.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_do_undo.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_earray.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_create.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_timetype.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_timestamps.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/__init__.py -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_expression.py -> build/lib.linux-x86_64-3.7/tables/tests
    creating build/lib.linux-x86_64-3.7/tables/nodes/tests
    copying tables/nodes/tests/test_filenode.py -> build/lib.linux-x86_64-3.7/tables/nodes/tests
    copying tables/nodes/tests/__init__.py -> build/lib.linux-x86_64-3.7/tables/nodes/tests
    copying tables/tests/smpl_compound_chunked.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/blosc_bigendian.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/oldflavor_numeric.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/non-chunked-table.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/bug-idx.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/indexes_2_0.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/issue_368.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/python2.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/python3.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/Tables_lzo1_shuffle.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/smpl_f64be.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/array_mdatom.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/float.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/scalar.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/zerodim-attrs-1.4.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/smpl_i32le.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/flavored_vlarrays-format1.6.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/nested-type-with-gaps.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/vlunicode_endian.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/issue_560.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/attr-u16.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/smpl_i32be.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/zerodim-attrs-1.3.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/smpl_enum.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/elink.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/smpl_f64le.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/smpl_SDSextendible.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/Tables_lzo2.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/idx-std-1.x.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/times-nested-be.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/Tables_lzo2_shuffle.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/Table2_1_lzo_nrv2e_shuffle.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/smpl_i64le.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/time-table-vlarray-1_x.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/smpl_i64be.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/slink.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/elink2.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/ex-noattr.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/Tables_lzo1.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/vlstr_attr.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/smpl_unsupptype.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_szip.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/indexes_2_1.h5 -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_ref_array1.mat -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/matlab_file.mat -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/tests/test_ref_array2.mat -> build/lib.linux-x86_64-3.7/tables/tests
    copying tables/nodes/tests/test_filenode.dat -> build/lib.linux-x86_64-3.7/tables/nodes/tests
    copying tables/nodes/tests/test_filenode.xbm -> build/lib.linux-x86_64-3.7/tables/nodes/tests
    copying tables/nodes/tests/test_filenode_v1.h5 -> build/lib.linux-x86_64-3.7/tables/nodes/tests
    running build_ext
    building 'tables.utilsextension' extension
    creating build/temp.linux-x86_64-3.7
    creating build/temp.linux-x86_64-3.7/tables
    creating build/temp.linux-x86_64-3.7/src
    creating build/temp.linux-x86_64-3.7/hdf5-blosc
    creating build/temp.linux-x86_64-3.7/hdf5-blosc/src
    creating build/temp.linux-x86_64-3.7/c-blosc
    creating build/temp.linux-x86_64-3.7/c-blosc/blosc
    creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs
    creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/lz4-1.8.1.2
    creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/snappy-1.1.1
    creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zlib-1.2.8
    creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4
    creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/common
    creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/decompress
    creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/compress
    creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/legacy
    creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/deprecated
    creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/dictBuilder
    /usr/bin/gcc-4.0 -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DNDEBUG=1 -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ihdf5-blosc/src -I/scratch/miniconda3/envs/genomedatatest/include -Ic-blosc/blosc -Ic-blosc/internal-complibs/lz4-1.8.1.2 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/zstd-1.3.4 -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/zstd-1.3.4/common -Ic-blosc/internal-complibs/zstd-1.3.4 -I/scratch/miniconda3/lib/python3.7/site-packages/numpy/core/include -I/scratch/miniconda3/include/python3.7m -c tables/utilsextension.c -o build/temp.linux-x86_64-3.7/tables/utilsextension.o -Isrc -DH5_USE_18_API -DH5Acreate_vers=2 -DH5Aiterate_vers=2 -DH5Dcreate_vers=2 -DH5Dopen_vers=2 -DH5Eclear_vers=2 -DH5Eprint_vers=2 -DH5Epush_vers=2 -DH5Eset_auto_vers=2 -DH5Eget_auto_vers=2 -DH5Ewalk_vers=2 -DH5E_auto_t_vers=2 -DH5Gcreate_vers=2 -DH5Gopen_vers=2 -DH5Pget_filter_vers=2 -DH5Pget_filter_by_id_vers=2 -DH5Tarray_create_vers=2 -DH5Tget_array_dims_vers=2 -DH5Z_class_t_vers=2 -DSHUFFLE_SSE2_ENABLED -msse2
    unable to execute '/usr/bin/gcc-4.0': No such file or directory
    error: command '/usr/bin/gcc-4.0' failed with exit status 1

    ----------------------------------------
Command "/scratch/miniconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-ms2r486i/tables/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-ognnh04e/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-ms2r486i/tables/
EricR86 commented 6 years ago

Original comment by Rachel Chan (Bitbucket: rcwchan).

Issue was with my ~/.profile searching for the wrong C compiler! Thanks!