Unable to install RGT completely

angla...@gmail.com

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Jun 24, 2020, 11:00:54 PM6/24/20

to RGT Users

Hi all,

I am new to bioinformatics and I am facing trouble downloading RGT or Reg-gen to my instance.

May I seek advice on how I can install these files?

Building wheel for pyBigWig (setup.py) ... error

ERROR: Command errored out with exit status 1:

command: /home/ubuntu/anaconda3/envs/my_env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-a0xos_yk/pyBigWig/setup.py'"'"'; __file__='"'"'/tmp/pip-install-a0xos_yk/pyBigWig/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-buutftqz

cwd: /tmp/pip-install-a0xos_yk/pyBigWig/

Complete output (36 lines):

/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'classifier'

warnings.warn(msg)

running bdist_wheel

running build

running build_py

creating build

creating build/lib.linux-x86_64-3.6

creating build/lib.linux-x86_64-3.6/pyBigWigTest

copying pyBigWigTest/__init__.py -> build/lib.linux-x86_64-3.6/pyBigWigTest

copying pyBigWigTest/test.py -> build/lib.linux-x86_64-3.6/pyBigWigTest

running egg_info

writing pyBigWig.egg-info/PKG-INFO

writing dependency_links to pyBigWig.egg-info/dependency_links.txt

writing requirements to pyBigWig.egg-info/requires.txt

writing top-level names to pyBigWig.egg-info/top_level.txt

reading manifest file 'pyBigWig.egg-info/SOURCES.txt'

reading manifest template 'MANIFEST.in'

writing manifest file 'pyBigWig.egg-info/SOURCES.txt'

copying pyBigWigTest/test.bigBed -> build/lib.linux-x86_64-3.6/pyBigWigTest

copying pyBigWigTest/test.bw -> build/lib.linux-x86_64-3.6/pyBigWigTest

running build_ext

building 'pyBigWig' extension

Warning: Can't read registry to find the necessary compiler setting

Make sure that Python modules winreg, win32api or win32con are installed.

C compiler: gcc -pthread -B /home/ubuntu/anaconda3/envs/my_env/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

creating build/temp.linux-x86_64-3.6

creating build/temp.linux-x86_64-3.6/libBigWig

compile options: '-DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -I/home/ubuntu/.local/lib/python3.6/site-packages/numpy/core/include -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -c'

gcc: pyBigWig.c

gcc: libBigWig/bwValues.c

gcc: libBigWig/bwWrite.c

gcc: libBigWig/bwStats.c

gcc: libBigWig/bwRead.c

gcc: libBigWig/io.c

error: Command "gcc -pthread -B /home/ubuntu/anaconda3/envs/my_env/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -I/home/ubuntu/.local/lib/python3.6/site-packages/numpy/core/include -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -c libBigWig/bwWrite.c -o build/temp.linux-x86_64-3.6/libBigWig/bwWrite.o" failed with exit status 127

----------------------------------------

ERROR: Failed building wheel for pyBigWig

Running setup.py clean for pyBigWig

Building wheel for PyVCF (setup.py) ... error

ERROR: Command errored out with exit status 1:

command: /home/ubuntu/anaconda3/envs/my_env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-a0xos_yk/PyVCF/setup.py'"'"'; __file__='"'"'/tmp/pip-install-a0xos_yk/PyVCF/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-vmm9wpyk

cwd: /tmp/pip-install-a0xos_yk/PyVCF/

Complete output (52 lines):

running bdist_wheel

running build

running build_py

creating build

creating build/lib.linux-x86_64-3.6

creating build/lib.linux-x86_64-3.6/vcf

copying vcf/__init__.py -> build/lib.linux-x86_64-3.6/vcf

copying vcf/sample_filter.py -> build/lib.linux-x86_64-3.6/vcf

copying vcf/utils.py -> build/lib.linux-x86_64-3.6/vcf

copying vcf/filters.py -> build/lib.linux-x86_64-3.6/vcf

copying vcf/model.py -> build/lib.linux-x86_64-3.6/vcf

copying vcf/parser.py -> build/lib.linux-x86_64-3.6/vcf

creating build/lib.linux-x86_64-3.6/vcf/test

copying vcf/test/__init__.py -> build/lib.linux-x86_64-3.6/vcf/test

copying vcf/test/test_vcf.py -> build/lib.linux-x86_64-3.6/vcf/test

copying vcf/test/prof.py -> build/lib.linux-x86_64-3.6/vcf/test

running egg_info

writing PyVCF.egg-info/PKG-INFO

writing dependency_links to PyVCF.egg-info/dependency_links.txt

writing entry points to PyVCF.egg-info/entry_points.txt

writing requirements to PyVCF.egg-info/requires.txt

writing top-level names to PyVCF.egg-info/top_level.txt

reading manifest file 'PyVCF.egg-info/SOURCES.txt'

reading manifest template 'MANIFEST.in'

writing manifest file 'PyVCF.egg-info/SOURCES.txt'

copying vcf/cparse.pyx -> build/lib.linux-x86_64-3.6/vcf

/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/site-packages/setuptools/lib2to3_ex.py:44: SetuptoolsDeprecationWarning: 2to3 support is deprecated. If the project still requires Python 2 support, please migrate to a single-codebase solution or employ an independent conversion process.

SetuptoolsDeprecationWarning)

Fixing build/lib.linux-x86_64-3.6/vcf/__init__.py build/lib.linux-x86_64-3.6/vcf/sample_filter.py build/lib.linux-x86_64-3.6/vcf/utils.py build/lib.linux-x86_64-3.6/vcf/filters.py build/lib.linux-x86_64-3.6/vcf/model.py build/lib.linux-x86_64-3.6/vcf/parser.py build/lib.linux-x86_64-3.6/vcf/test/__init__.py build/lib.linux-x86_64-3.6/vcf/test/test_vcf.py build/lib.linux-x86_64-3.6/vcf/test/prof.py

Skipping optional fixer: buffer

Skipping optional fixer: idioms

Skipping optional fixer: set_literal

Skipping optional fixer: ws_comma

Fixing build/lib.linux-x86_64-3.6/vcf/__init__.py build/lib.linux-x86_64-3.6/vcf/sample_filter.py build/lib.linux-x86_64-3.6/vcf/utils.py build/lib.linux-x86_64-3.6/vcf/filters.py build/lib.linux-x86_64-3.6/vcf/model.py build/lib.linux-x86_64-3.6/vcf/parser.py build/lib.linux-x86_64-3.6/vcf/test/__init__.py build/lib.linux-x86_64-3.6/vcf/test/test_vcf.py build/lib.linux-x86_64-3.6/vcf/test/prof.py

Skipping optional fixer: buffer

Skipping optional fixer: idioms

Skipping optional fixer: set_literal

Skipping optional fixer: ws_comma

running build_ext

cythoning vcf/cparse.pyx to vcf/cparse.c

/home/ubuntu/.local/lib/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-install-a0xos_yk/PyVCF/vcf/cparse.pyx

tree = Parsing.p_module(s, pxd, full_module_name)

warning: vcf/cparse.pyx:16:14: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.

warning: vcf/cparse.pyx:16:21: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.

warning: vcf/cparse.pyx:16:27: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.

warning: vcf/cparse.pyx:16:40: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.

building 'vcf.cparse' extension

creating build/temp.linux-x86_64-3.6

creating build/temp.linux-x86_64-3.6/vcf

gcc -pthread -B /home/ubuntu/anaconda3/envs/my_env/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -c vcf/cparse.c -o build/temp.linux-x86_64-3.6/vcf/cparse.o

unable to execute 'gcc': No such file or directory

error: command 'gcc' failed with exit status 1

----------------------------------------

ERROR: Failed building wheel for PyVCF

Running setup.py clean for PyVCF

Building wheel for fisher (setup.py) ... error

ERROR: Command errored out with exit status 1:

command: /home/ubuntu/anaconda3/envs/my_env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-a0xos_yk/fisher/setup.py'"'"'; __file__='"'"'/tmp/pip-install-a0xos_yk/fisher/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-8ji97ain

cwd: /tmp/pip-install-a0xos_yk/fisher/

Complete output (20 lines):

/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/site-packages/setuptools/dist.py:454: UserWarning: Normalizing 'v0.1.9' to '0.1.9'

warnings.warn(tmpl.format(**locals()))

running bdist_wheel

running build

running build_py

creating build

creating build/lib.linux-x86_64-3.6

creating build/lib.linux-x86_64-3.6/fisher

copying fisher/__init__.py -> build/lib.linux-x86_64-3.6/fisher

copying fisher/tableprinter.py -> build/lib.linux-x86_64-3.6/fisher

copying fisher/_version.py -> build/lib.linux-x86_64-3.6/fisher

UPDATING build/lib.linux-x86_64-3.6/fisher/_version.py

set build/lib.linux-x86_64-3.6/fisher/_version.py to 'v0.1.9'

running build_ext

building 'fisher.cfisher' extension

creating build/temp.linux-x86_64-3.6

creating build/temp.linux-x86_64-3.6/src

gcc -pthread -B /home/ubuntu/anaconda3/envs/my_env/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -I/home/ubuntu/.local/lib/python3.6/site-packages/numpy/core/include -c src/cfisher.c -o build/temp.linux-x86_64-3.6/src/cfisher.o -O3

unable to execute 'gcc': No such file or directory

error: command 'gcc' failed with exit status 1

----------------------------------------

ERROR: Failed building wheel for fisher

Running setup.py clean for fisher

Building wheel for moods-python (setup.py) ... error

ERROR: Command errored out with exit status 1:

command: /home/ubuntu/anaconda3/envs/my_env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-a0xos_yk/moods-python/setup.py'"'"'; __file__='"'"'/tmp/pip-install-a0xos_yk/moods-python/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-c1vx9gpx

cwd: /tmp/pip-install-a0xos_yk/moods-python/

Complete output (18 lines):

running bdist_wheel

running build

running build_py

creating build

creating build/lib.linux-x86_64-3.6

creating build/lib.linux-x86_64-3.6/MOODS

copying MOODS/__init__.py -> build/lib.linux-x86_64-3.6/MOODS

copying MOODS/parsers.py -> build/lib.linux-x86_64-3.6/MOODS

copying MOODS/tools.py -> build/lib.linux-x86_64-3.6/MOODS

copying MOODS/scan.py -> build/lib.linux-x86_64-3.6/MOODS

copying MOODS/misc.py -> build/lib.linux-x86_64-3.6/MOODS

running build_ext

building 'MOODS._tools' extension

creating build/temp.linux-x86_64-3.6

creating build/temp.linux-x86_64-3.6/core

gcc -pthread -B /home/ubuntu/anaconda3/envs/my_env/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Icore/ -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -c core/tools_wrap.cxx -o build/temp.linux-x86_64-3.6/core/tools_wrap.o -march=native -O3 -fPIC --std=c++11

unable to execute 'gcc': No such file or directory

error: command 'gcc' failed with exit status 1

----------------------------------------

ERROR: Failed building wheel for moods-python

Running setup.py clean for moods-python

Building wheel for hmmlearn (setup.py) ... error

ERROR: Command errored out with exit status 1:

command: /home/ubuntu/anaconda3/envs/my_env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-a0xos_yk/hmmlearn/setup.py'"'"'; __file__='"'"'/tmp/pip-install-a0xos_yk/hmmlearn/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-kx5cudfr

cwd: /tmp/pip-install-a0xos_yk/hmmlearn/

Complete output (24 lines):

running bdist_wheel

running build

running build_py

creating build

creating build/lib.linux-x86_64-3.6

creating build/lib.linux-x86_64-3.6/hmmlearn

copying lib/hmmlearn/__init__.py -> build/lib.linux-x86_64-3.6/hmmlearn

copying lib/hmmlearn/base.py -> build/lib.linux-x86_64-3.6/hmmlearn

copying lib/hmmlearn/stats.py -> build/lib.linux-x86_64-3.6/hmmlearn

copying lib/hmmlearn/_utils.py -> build/lib.linux-x86_64-3.6/hmmlearn

copying lib/hmmlearn/utils.py -> build/lib.linux-x86_64-3.6/hmmlearn

copying lib/hmmlearn/hmm.py -> build/lib.linux-x86_64-3.6/hmmlearn

copying lib/hmmlearn/_version.py -> build/lib.linux-x86_64-3.6/hmmlearn

creating build/lib.linux-x86_64-3.6/hmmlearn/tests

copying lib/hmmlearn/tests/test_gmm_hmm_new.py -> build/lib.linux-x86_64-3.6/hmmlearn/tests

copying lib/hmmlearn/tests/__init__.py -> build/lib.linux-x86_64-3.6/hmmlearn/tests

copying lib/hmmlearn/tests/test_utils.py -> build/lib.linux-x86_64-3.6/hmmlearn/tests

copying lib/hmmlearn/tests/conftest.py -> build/lib.linux-x86_64-3.6/hmmlearn/tests

copying lib/hmmlearn/tests/test_gmm_hmm.py -> build/lib.linux-x86_64-3.6/hmmlearn/tests

copying lib/hmmlearn/tests/test_gaussian_hmm.py -> build/lib.linux-x86_64-3.6/hmmlearn/tests

copying lib/hmmlearn/tests/test_base.py -> build/lib.linux-x86_64-3.6/hmmlearn/tests

copying lib/hmmlearn/tests/test_multinomial_hmm.py -> build/lib.linux-x86_64-3.6/hmmlearn/tests

running build_ext

error: Command "gcc -pthread -B /home/ubuntu/anaconda3/envs/my_env/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/home/ubuntu/.local/lib/python3.6/site-packages/numpy/core/include -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -c lib/hmmlearn/_hmmc.c -o build/temp.linux-x86_64-3.6/lib/hmmlearn/_hmmc.o" failed with exit status 127

----------------------------------------

ERROR: Failed building wheel for hmmlearn

Running setup.py clean for hmmlearn

Building wheel for pyx (setup.py) ... done

Created wheel for pyx: filename=PyX-0.15-py3-none-any.whl size=434892 sha256=81705bee4b1350349ea4db24c26723467bdd6dd35dc8c4dccf112e89fe5a9619

Stored in directory: /home/ubuntu/.cache/pip/wheels/40/80/54/de46d51596161afdb374db4cdfa2baf63446ccf5035c6a8b38

Building wheel for mpmath (setup.py) ... done

Created wheel for mpmath: filename=mpmath-1.1.0-py3-none-any.whl size=532239 sha256=895158e44ee929e22171e7b66a4b3fed29e32ebab9e3f506050b8606ac2a607c

Stored in directory: /home/ubuntu/.cache/pip/wheels/e8/38/69/aa17553ad31f09ff5fa44c8a1a6c5b47e7c9261e9c7c16b9fb

Building wheel for matplotlib-venn (setup.py) ... done

Created wheel for matplotlib-venn: filename=matplotlib_venn-0.11.5-py3-none-any.whl size=32394 sha256=06f52fc176e7b8a632f82e8a329004d8a6defc96da63b5ef124cc50022d9e784

Stored in directory: /home/ubuntu/.cache/pip/wheels/9d/6e/6c/9338bc6bbd01bc676b2e30371a5a931385649c7ed8c503a9b6

Successfully built pyx mpmath matplotlib-venn

Failed to build pyBigWig PyVCF fisher moods-python hmmlearn

Installing collected packages: pysam, pyBigWig, PyVCF, Biopython, fisher, moods-python, joblib, threadpoolctl, scikit-learn, hmmlearn, pytz, six, python-dateutil, pandas, cycler, kiwisolver, pyparsing, matplotlib, logomaker, pyx, mpmath, HTSeq, matplotlib-venn, natsort, RGT

Running setup.py install for pyBigWig ... error

ERROR: Command errored out with exit status 1:

command: /home/ubuntu/anaconda3/envs/my_env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-a0xos_yk/pyBigWig/setup.py'"'"'; __file__='"'"'/tmp/pip-install-a0xos_yk/pyBigWig/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-45zth63l/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/ubuntu/.local/include/python3.6m/pyBigWig

cwd: /tmp/pip-install-a0xos_yk/pyBigWig/

Complete output (36 lines):

/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'classifier'

warnings.warn(msg)

running install

running build

running build_py

creating build

creating build/lib.linux-x86_64-3.6

creating build/lib.linux-x86_64-3.6/pyBigWigTest

copying pyBigWigTest/__init__.py -> build/lib.linux-x86_64-3.6/pyBigWigTest

copying pyBigWigTest/test.py -> build/lib.linux-x86_64-3.6/pyBigWigTest

running egg_info

writing pyBigWig.egg-info/PKG-INFO

writing dependency_links to pyBigWig.egg-info/dependency_links.txt

writing requirements to pyBigWig.egg-info/requires.txt

writing top-level names to pyBigWig.egg-info/top_level.txt

reading manifest file 'pyBigWig.egg-info/SOURCES.txt'

reading manifest template 'MANIFEST.in'

writing manifest file 'pyBigWig.egg-info/SOURCES.txt'

copying pyBigWigTest/test.bigBed -> build/lib.linux-x86_64-3.6/pyBigWigTest

copying pyBigWigTest/test.bw -> build/lib.linux-x86_64-3.6/pyBigWigTest

running build_ext

building 'pyBigWig' extension

Warning: Can't read registry to find the necessary compiler setting

Make sure that Python modules winreg, win32api or win32con are installed.

C compiler: gcc -pthread -B /home/ubuntu/anaconda3/envs/my_env/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

creating build/temp.linux-x86_64-3.6

creating build/temp.linux-x86_64-3.6/libBigWig

compile options: '-DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -I/home/ubuntu/.local/lib/python3.6/site-packages/numpy/core/include -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -c'

gcc: libBigWig/bwRead.c

gcc: libBigWig/io.c

gcc: libBigWig/bwWrite.c

gcc: libBigWig/bwValues.c

gcc: pyBigWig.c

gcc: libBigWig/bwStats.c

error: Command "gcc -pthread -B /home/ubuntu/anaconda3/envs/my_env/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -I/home/ubuntu/.local/lib/python3.6/site-packages/numpy/core/include -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -c libBigWig/bwWrite.c -o build/temp.linux-x86_64-3.6/libBigWig/bwWrite.o" failed with exit status 127

----------------------------------------

ERROR: Command errored out with exit status 1: /home/ubuntu/anaconda3/envs/my_env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-a0xos_yk/pyBigWig/setup.py'"'"'; __file__='"'"'/tmp/pip-install-a0xos_yk/pyBigWig/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-45zth63l/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/ubuntu/.local/include/python3.6m/pyBigWig Check the logs for full command output.

(my_env) ubuntu@ip-172-31-24-191:~$ pip install --user pyBigWig==0.3.12

Collecting pyBigWig==0.3.12

Using cached pyBigWig-0.3.12.tar.gz (66 kB)

Building wheels for collected packages: pyBigWig

Building wheel for pyBigWig (setup.py) ... error

ERROR: Command errored out with exit status 1:

command: /home/ubuntu/anaconda3/envs/my_env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-b_oskdrr/pyBigWig/setup.py'"'"'; __file__='"'"'/tmp/pip-install-b_oskdrr/pyBigWig/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-jgtw3920

cwd: /tmp/pip-install-b_oskdrr/pyBigWig/

Complete output (36 lines):

/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'classifier'

warnings.warn(msg)

running bdist_wheel

running build

running build_py

creating build

creating build/lib.linux-x86_64-3.6

creating build/lib.linux-x86_64-3.6/pyBigWigTest

copying pyBigWigTest/__init__.py -> build/lib.linux-x86_64-3.6/pyBigWigTest

copying pyBigWigTest/test.py -> build/lib.linux-x86_64-3.6/pyBigWigTest

running egg_info

writing pyBigWig.egg-info/PKG-INFO

writing dependency_links to pyBigWig.egg-info/dependency_links.txt

writing requirements to pyBigWig.egg-info/requires.txt

writing top-level names to pyBigWig.egg-info/top_level.txt

reading manifest file 'pyBigWig.egg-info/SOURCES.txt'

reading manifest template 'MANIFEST.in'

writing manifest file 'pyBigWig.egg-info/SOURCES.txt'

copying pyBigWigTest/test.bigBed -> build/lib.linux-x86_64-3.6/pyBigWigTest

copying pyBigWigTest/test.bw -> build/lib.linux-x86_64-3.6/pyBigWigTest

running build_ext

building 'pyBigWig' extension

Warning: Can't read registry to find the necessary compiler setting

Make sure that Python modules winreg, win32api or win32con are installed.

C compiler: gcc -pthread -B /home/ubuntu/anaconda3/envs/my_env/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

creating build/temp.linux-x86_64-3.6

creating build/temp.linux-x86_64-3.6/libBigWig

compile options: '-DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -I/home/ubuntu/.local/lib/python3.6/site-packages/numpy/core/include -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -c'

gcc: libBigWig/bwWrite.c

gcc: libBigWig/bwRead.c

gcc: libBigWig/bwStats.c

gcc: pyBigWig.c

gcc: libBigWig/io.c

gcc: libBigWig/bwValues.c

error: Command "gcc -pthread -B /home/ubuntu/anaconda3/envs/my_env/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -I/home/ubuntu/.local/lib/python3.6/site-packages/numpy/core/include -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -c libBigWig/bwStats.c -o build/temp.linux-x86_64-3.6/libBigWig/bwStats.o" failed with exit status 127

----------------------------------------

ERROR: Failed building wheel for pyBigWig

Running setup.py clean for pyBigWig

Failed to build pyBigWig

Installing collected packages: pyBigWig

Running setup.py install for pyBigWig ... error

ERROR: Command errored out with exit status 1:

command: /home/ubuntu/anaconda3/envs/my_env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-b_oskdrr/pyBigWig/setup.py'"'"'; __file__='"'"'/tmp/pip-install-b_oskdrr/pyBigWig/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-satwtr_7/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/ubuntu/.local/include/python3.6m/pyBigWig

cwd: /tmp/pip-install-b_oskdrr/pyBigWig/

Complete output (36 lines):

/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'classifier'

warnings.warn(msg)

running install

running build

running build_py

creating build

creating build/lib.linux-x86_64-3.6

creating build/lib.linux-x86_64-3.6/pyBigWigTest

copying pyBigWigTest/__init__.py -> build/lib.linux-x86_64-3.6/pyBigWigTest

copying pyBigWigTest/test.py -> build/lib.linux-x86_64-3.6/pyBigWigTest

running egg_info

writing pyBigWig.egg-info/PKG-INFO

writing dependency_links to pyBigWig.egg-info/dependency_links.txt

writing requirements to pyBigWig.egg-info/requires.txt

writing top-level names to pyBigWig.egg-info/top_level.txt

reading manifest file 'pyBigWig.egg-info/SOURCES.txt'

reading manifest template 'MANIFEST.in'

writing manifest file 'pyBigWig.egg-info/SOURCES.txt'

copying pyBigWigTest/test.bigBed -> build/lib.linux-x86_64-3.6/pyBigWigTest

copying pyBigWigTest/test.bw -> build/lib.linux-x86_64-3.6/pyBigWigTest

running build_ext

building 'pyBigWig' extension

Warning: Can't read registry to find the necessary compiler setting

Make sure that Python modules winreg, win32api or win32con are installed.

C compiler: gcc -pthread -B /home/ubuntu/anaconda3/envs/my_env/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

creating build/temp.linux-x86_64-3.6

creating build/temp.linux-x86_64-3.6/libBigWig

compile options: '-DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -I/home/ubuntu/.local/lib/python3.6/site-packages/numpy/core/include -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -c'

gcc: libBigWig/bwWrite.c

gcc: libBigWig/bwValues.c

gcc: libBigWig/io.c

gcc: pyBigWig.c

gcc: libBigWig/bwStats.c

gcc: libBigWig/bwRead.c

error: Command "gcc -pthread -B /home/ubuntu/anaconda3/envs/my_env/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -I/home/ubuntu/.local/lib/python3.6/site-packages/numpy/core/include -I/home/ubuntu/anaconda3/envs/my_env/include/python3.6m -c libBigWig/bwValues.c -o build/temp.linux-x86_64-3.6/libBigWig/bwValues.o" failed with exit status 127

----------------------------------------

ERROR: Command errored out with exit status 1: /home/ubuntu/anaconda3/envs/my_env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-b_oskdrr/pyBigWig/setup.py'"'"'; __file__='"'"'/tmp/pip-install-b_oskdrr/pyBigWig/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-satwtr_7/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/ubuntu/.local/include/python3.6m/pyBigWig Check the logs for full command output.

(my_env) ubuntu@ip-172-31-24-191:~$ rgt-hont

rgt-hont: command not found

(my_env) ubuntu@ip-172-31-24-191:~$ rgt-hint

rgt-hint: command not found

(my_env) ubuntu@ip-172-31-24-191:~$ ls -1

Data

anaconda3

aws

awscliv2.zip

proj

reg-gen

rgtdata

(my_env) ubuntu@ip-172-31-24-191:~$ /home/ubuntu/reg-gen/rgt-hint footprinting

-bash: /home/ubuntu/reg-gen/rgt-hint: No such file or directory

(my_env) ubuntu@ip-172-31-24-191:~$ cd reg-gen

(my_env) ubuntu@ip-172-31-24-191:~/reg-gen$ python setup.py install --user

['data/bin/linux/bedToBigBed', 'data/bin/linux/bigBedToBed', 'data/bin/linux/wigToBigWig', 'data/bin/linux/bigWigMerge', 'data/bin/linux/bedGraphToBigWig']

['data/bin/linux/bedToBigBed', 'data/bin/linux/bigBedToBed']

[]

['data/bin/linux/wigToBigWig', 'data/bin/linux/bigWigMerge', 'data/bin/linux/bedGraphToBigWig']

[]

running install

running bdist_egg

running egg_info

creating RGT.egg-info

writing RGT.egg-info/PKG-INFO

writing dependency_links to RGT.egg-info/dependency_links.txt

writing entry points to RGT.egg-info/entry_points.txt

writing requirements to RGT.egg-info/requires.txt

writing top-level names to RGT.egg-info/top_level.txt

writing manifest file 'RGT.egg-info/SOURCES.txt'

reading manifest file 'RGT.egg-info/SOURCES.txt'

reading manifest template 'MANIFEST.in'

writing manifest file 'RGT.egg-info/SOURCES.txt'

installing library code to build/bdist.linux-x86_64/egg

running install_lib

running build_py

creating build

creating build/lib

creating build/lib/rgt

copying rgt/GenomicRegionSet.py -> build/lib/rgt

copying rgt/GenomicVariant.py -> build/lib/rgt

copying rgt/ExperimentalMatrix.py -> build/lib/rgt

copying rgt/__init__.py -> build/lib/rgt

copying rgt/AnnotationSet.py -> build/lib/rgt

copying rgt/SequenceSet.py -> build/lib/rgt

copying rgt/CoverageSet.py -> build/lib/rgt

copying rgt/Util.py -> build/lib/rgt

copying rgt/GeneSet.py -> build/lib/rgt

copying rgt/__version__.py -> build/lib/rgt

copying rgt/helper.py -> build/lib/rgt

copying rgt/GenomicRegion.py -> build/lib/rgt

copying rgt/GenomicVariantSet.py -> build/lib/rgt

copying rgt/MotifSet.py -> build/lib/rgt

creating build/lib/rgt/filterVCF

copying rgt/filterVCF/__init__.py -> build/lib/rgt/filterVCF

copying rgt/filterVCF/filterVCF.py -> build/lib/rgt/filterVCF

copying rgt/filterVCF/max_density.py -> build/lib/rgt/filterVCF

creating build/lib/rgt/THOR

copying rgt/THOR/__init__.py -> build/lib/rgt/THOR

copying rgt/THOR/normalize.py -> build/lib/rgt/THOR

copying rgt/THOR/RegionGiver.py -> build/lib/rgt/THOR

copying rgt/THOR/get_fast_gen_pvalue.py -> build/lib/rgt/THOR

copying rgt/THOR/postprocessing.py -> build/lib/rgt/THOR

copying rgt/THOR/DualCoverageSet.py -> build/lib/rgt/THOR

copying rgt/THOR/norm_genelevel.py -> build/lib/rgt/THOR

copying rgt/THOR/neg_bin.py -> build/lib/rgt/THOR

copying rgt/THOR/binom_hmm.py -> build/lib/rgt/THOR

copying rgt/THOR/tracker.py -> build/lib/rgt/THOR

copying rgt/THOR/MultiCoverageSet.py -> build/lib/rgt/THOR

copying rgt/THOR/get_extension_size.py -> build/lib/rgt/THOR

copying rgt/THOR/dpc_help.py -> build/lib/rgt/THOR

copying rgt/THOR/input_parser.py -> build/lib/rgt/THOR

copying rgt/THOR/neg_bin_rep_hmm.py -> build/lib/rgt/THOR

copying rgt/THOR/THOR.py -> build/lib/rgt/THOR

copying rgt/THOR/help_hmm.py -> build/lib/rgt/THOR

creating build/lib/rgt/tdf

copying rgt/tdf/triplexTools.py -> build/lib/rgt/tdf

copying rgt/tdf/__init__.py -> build/lib/rgt/tdf

copying rgt/tdf/Statistics.py -> build/lib/rgt/tdf

copying rgt/tdf/Main.py -> build/lib/rgt/tdf

copying rgt/tdf/Report.py -> build/lib/rgt/tdf

copying rgt/tdf/Triplexes.py -> build/lib/rgt/tdf

copying rgt/tdf/RNADNABindingSet.py -> build/lib/rgt/tdf

copying rgt/tdf/Input.py -> build/lib/rgt/tdf

copying rgt/tdf/BindingSiteSet.py -> build/lib/rgt/tdf

creating build/lib/rgt/HINT

copying rgt/HINT/biasTable.py -> build/lib/rgt/HINT

copying rgt/HINT/__init__.py -> build/lib/rgt/HINT

copying rgt/HINT/Footprinting.py -> build/lib/rgt/HINT

copying rgt/HINT/Main.py -> build/lib/rgt/HINT

copying rgt/HINT/pileupRegion.py -> build/lib/rgt/HINT

copying rgt/HINT/Tracks.py -> build/lib/rgt/HINT

copying rgt/HINT/hmm.py -> build/lib/rgt/HINT

copying rgt/HINT/Evaluation.py -> build/lib/rgt/HINT

copying rgt/HINT/Estimation.py -> build/lib/rgt/HINT

copying rgt/HINT/Training.py -> build/lib/rgt/HINT

copying rgt/HINT/signalProcessing.py -> build/lib/rgt/HINT

copying rgt/HINT/DifferentialAnalysis.py -> build/lib/rgt/HINT

copying rgt/HINT/Evidence.py -> build/lib/rgt/HINT

copying rgt/HINT/Plotting.py -> build/lib/rgt/HINT

creating build/lib/rgt/motifanalysis

copying rgt/motifanalysis/Mapper.py -> build/lib/rgt/motifanalysis

copying rgt/motifanalysis/Match.py -> build/lib/rgt/motifanalysis

copying rgt/motifanalysis/__init__.py -> build/lib/rgt/motifanalysis

copying rgt/motifanalysis/Statistics.py -> build/lib/rgt/motifanalysis

copying rgt/motifanalysis/Util.py -> build/lib/rgt/motifanalysis

copying rgt/motifanalysis/Main.py -> build/lib/rgt/motifanalysis

copying rgt/motifanalysis/Enrichment.py -> build/lib/rgt/motifanalysis

copying rgt/motifanalysis/Motif.py -> build/lib/rgt/motifanalysis

creating build/lib/rgt/viz

copying rgt/viz/lineplot.py -> build/lib/rgt/viz

copying rgt/viz/__init__.py -> build/lib/rgt/viz

copying rgt/viz/combinatorial_test.py -> build/lib/rgt/viz

copying rgt/viz/shared_function.py -> build/lib/rgt/viz

copying rgt/viz/Main.py -> build/lib/rgt/viz

copying rgt/viz/boxplot.py -> build/lib/rgt/viz

copying rgt/viz/jaccard_test.py -> build/lib/rgt/viz

copying rgt/viz/bed_profile.py -> build/lib/rgt/viz

copying rgt/viz/plotTools.py -> build/lib/rgt/viz

copying rgt/viz/projection_test.py -> build/lib/rgt/viz

copying rgt/viz/intersection_test.py -> build/lib/rgt/viz

creating build/bdist.linux-x86_64

creating build/bdist.linux-x86_64/egg

creating build/bdist.linux-x86_64/egg/rgt

copying build/lib/rgt/GenomicRegionSet.py -> build/bdist.linux-x86_64/egg/rgt

copying build/lib/rgt/GenomicVariant.py -> build/bdist.linux-x86_64/egg/rgt

copying build/lib/rgt/ExperimentalMatrix.py -> build/bdist.linux-x86_64/egg/rgt

copying build/lib/rgt/__init__.py -> build/bdist.linux-x86_64/egg/rgt

copying build/lib/rgt/AnnotationSet.py -> build/bdist.linux-x86_64/egg/rgt

creating build/bdist.linux-x86_64/egg/rgt/filterVCF

copying build/lib/rgt/filterVCF/__init__.py -> build/bdist.linux-x86_64/egg/rgt/filterVCF

copying build/lib/rgt/filterVCF/filterVCF.py -> build/bdist.linux-x86_64/egg/rgt/filterVCF

copying build/lib/rgt/filterVCF/max_density.py -> build/bdist.linux-x86_64/egg/rgt/filterVCF

copying build/lib/rgt/SequenceSet.py -> build/bdist.linux-x86_64/egg/rgt

creating build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/THOR/__init__.py -> build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/THOR/normalize.py -> build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/THOR/RegionGiver.py -> build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/THOR/get_fast_gen_pvalue.py -> build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/THOR/postprocessing.py -> build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/THOR/DualCoverageSet.py -> build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/THOR/norm_genelevel.py -> build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/THOR/neg_bin.py -> build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/THOR/binom_hmm.py -> build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/THOR/tracker.py -> build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/THOR/MultiCoverageSet.py -> build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/THOR/get_extension_size.py -> build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/THOR/dpc_help.py -> build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/THOR/input_parser.py -> build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/THOR/neg_bin_rep_hmm.py -> build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/THOR/THOR.py -> build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/THOR/help_hmm.py -> build/bdist.linux-x86_64/egg/rgt/THOR

copying build/lib/rgt/CoverageSet.py -> build/bdist.linux-x86_64/egg/rgt

creating build/bdist.linux-x86_64/egg/rgt/tdf

copying build/lib/rgt/tdf/triplexTools.py -> build/bdist.linux-x86_64/egg/rgt/tdf

copying build/lib/rgt/tdf/__init__.py -> build/bdist.linux-x86_64/egg/rgt/tdf

copying build/lib/rgt/tdf/Statistics.py -> build/bdist.linux-x86_64/egg/rgt/tdf

copying build/lib/rgt/tdf/Main.py -> build/bdist.linux-x86_64/egg/rgt/tdf

copying build/lib/rgt/tdf/Report.py -> build/bdist.linux-x86_64/egg/rgt/tdf

copying build/lib/rgt/tdf/Triplexes.py -> build/bdist.linux-x86_64/egg/rgt/tdf

copying build/lib/rgt/tdf/RNADNABindingSet.py -> build/bdist.linux-x86_64/egg/rgt/tdf

copying build/lib/rgt/tdf/Input.py -> build/bdist.linux-x86_64/egg/rgt/tdf

copying build/lib/rgt/tdf/BindingSiteSet.py -> build/bdist.linux-x86_64/egg/rgt/tdf

copying build/lib/rgt/Util.py -> build/bdist.linux-x86_64/egg/rgt

copying build/lib/rgt/GeneSet.py -> build/bdist.linux-x86_64/egg/rgt

creating build/bdist.linux-x86_64/egg/rgt/HINT

copying build/lib/rgt/HINT/biasTable.py -> build/bdist.linux-x86_64/egg/rgt/HINT

copying build/lib/rgt/HINT/__init__.py -> build/bdist.linux-x86_64/egg/rgt/HINT

copying build/lib/rgt/HINT/Footprinting.py -> build/bdist.linux-x86_64/egg/rgt/HINT

copying build/lib/rgt/HINT/Main.py -> build/bdist.linux-x86_64/egg/rgt/HINT

copying build/lib/rgt/HINT/pileupRegion.py -> build/bdist.linux-x86_64/egg/rgt/HINT

copying build/lib/rgt/HINT/Tracks.py -> build/bdist.linux-x86_64/egg/rgt/HINT

copying build/lib/rgt/HINT/hmm.py -> build/bdist.linux-x86_64/egg/rgt/HINT

copying build/lib/rgt/HINT/Evaluation.py -> build/bdist.linux-x86_64/egg/rgt/HINT

copying build/lib/rgt/HINT/Estimation.py -> build/bdist.linux-x86_64/egg/rgt/HINT

copying build/lib/rgt/HINT/Training.py -> build/bdist.linux-x86_64/egg/rgt/HINT

copying build/lib/rgt/HINT/signalProcessing.py -> build/bdist.linux-x86_64/egg/rgt/HINT

copying build/lib/rgt/HINT/DifferentialAnalysis.py -> build/bdist.linux-x86_64/egg/rgt/HINT

copying build/lib/rgt/HINT/Evidence.py -> build/bdist.linux-x86_64/egg/rgt/HINT

copying build/lib/rgt/HINT/Plotting.py -> build/bdist.linux-x86_64/egg/rgt/HINT

creating build/bdist.linux-x86_64/egg/rgt/motifanalysis

copying build/lib/rgt/motifanalysis/Mapper.py -> build/bdist.linux-x86_64/egg/rgt/motifanalysis

copying build/lib/rgt/motifanalysis/Match.py -> build/bdist.linux-x86_64/egg/rgt/motifanalysis

copying build/lib/rgt/motifanalysis/__init__.py -> build/bdist.linux-x86_64/egg/rgt/motifanalysis

copying build/lib/rgt/motifanalysis/Statistics.py -> build/bdist.linux-x86_64/egg/rgt/motifanalysis

copying build/lib/rgt/motifanalysis/Util.py -> build/bdist.linux-x86_64/egg/rgt/motifanalysis

copying build/lib/rgt/motifanalysis/Main.py -> build/bdist.linux-x86_64/egg/rgt/motifanalysis

copying build/lib/rgt/motifanalysis/Enrichment.py -> build/bdist.linux-x86_64/egg/rgt/motifanalysis

copying build/lib/rgt/motifanalysis/Motif.py -> build/bdist.linux-x86_64/egg/rgt/motifanalysis

copying build/lib/rgt/__version__.py -> build/bdist.linux-x86_64/egg/rgt

copying build/lib/rgt/helper.py -> build/bdist.linux-x86_64/egg/rgt

creating build/bdist.linux-x86_64/egg/rgt/viz

copying build/lib/rgt/viz/lineplot.py -> build/bdist.linux-x86_64/egg/rgt/viz

copying build/lib/rgt/viz/__init__.py -> build/bdist.linux-x86_64/egg/rgt/viz

copying build/lib/rgt/viz/combinatorial_test.py -> build/bdist.linux-x86_64/egg/rgt/viz

copying build/lib/rgt/viz/shared_function.py -> build/bdist.linux-x86_64/egg/rgt/viz

copying build/lib/rgt/viz/Main.py -> build/bdist.linux-x86_64/egg/rgt/viz

copying build/lib/rgt/viz/boxplot.py -> build/bdist.linux-x86_64/egg/rgt/viz

copying build/lib/rgt/viz/jaccard_test.py -> build/bdist.linux-x86_64/egg/rgt/viz

copying build/lib/rgt/viz/bed_profile.py -> build/bdist.linux-x86_64/egg/rgt/viz

copying build/lib/rgt/viz/plotTools.py -> build/bdist.linux-x86_64/egg/rgt/viz

copying build/lib/rgt/viz/projection_test.py -> build/bdist.linux-x86_64/egg/rgt/viz

copying build/lib/rgt/viz/intersection_test.py -> build/bdist.linux-x86_64/egg/rgt/viz

copying build/lib/rgt/GenomicRegion.py -> build/bdist.linux-x86_64/egg/rgt

copying build/lib/rgt/GenomicVariantSet.py -> build/bdist.linux-x86_64/egg/rgt

copying build/lib/rgt/MotifSet.py -> build/bdist.linux-x86_64/egg/rgt

byte-compiling build/bdist.linux-x86_64/egg/rgt/GenomicRegionSet.py to GenomicRegionSet.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/GenomicVariant.py to GenomicVariant.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/ExperimentalMatrix.py to ExperimentalMatrix.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/__init__.py to __init__.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/AnnotationSet.py to AnnotationSet.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/filterVCF/__init__.py to __init__.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/filterVCF/filterVCF.py to filterVCF.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/filterVCF/max_density.py to max_density.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/SequenceSet.py to SequenceSet.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/THOR/__init__.py to __init__.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/THOR/normalize.py to normalize.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/THOR/RegionGiver.py to RegionGiver.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/THOR/get_fast_gen_pvalue.py to get_fast_gen_pvalue.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/THOR/postprocessing.py to postprocessing.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/THOR/DualCoverageSet.py to DualCoverageSet.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/THOR/norm_genelevel.py to norm_genelevel.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/THOR/neg_bin.py to neg_bin.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/THOR/binom_hmm.py to binom_hmm.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/THOR/tracker.py to tracker.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/THOR/MultiCoverageSet.py to MultiCoverageSet.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/THOR/get_extension_size.py to get_extension_size.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/THOR/dpc_help.py to dpc_help.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/THOR/input_parser.py to input_parser.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/THOR/neg_bin_rep_hmm.py to neg_bin_rep_hmm.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/THOR/THOR.py to THOR.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/THOR/help_hmm.py to help_hmm.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/CoverageSet.py to CoverageSet.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/tdf/triplexTools.py to triplexTools.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/tdf/__init__.py to __init__.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/tdf/Statistics.py to Statistics.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/tdf/Main.py to Main.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/tdf/Report.py to Report.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/tdf/Triplexes.py to Triplexes.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/tdf/RNADNABindingSet.py to RNADNABindingSet.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/tdf/Input.py to Input.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/tdf/BindingSiteSet.py to BindingSiteSet.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/Util.py to Util.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/GeneSet.py to GeneSet.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/HINT/biasTable.py to biasTable.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/HINT/__init__.py to __init__.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/HINT/Footprinting.py to Footprinting.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/HINT/Main.py to Main.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/HINT/pileupRegion.py to pileupRegion.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/HINT/Tracks.py to Tracks.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/HINT/hmm.py to hmm.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/HINT/Evaluation.py to Evaluation.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/HINT/Estimation.py to Estimation.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/HINT/Training.py to Training.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/HINT/signalProcessing.py to signalProcessing.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/HINT/DifferentialAnalysis.py to DifferentialAnalysis.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/HINT/Evidence.py to Evidence.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/HINT/Plotting.py to Plotting.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/motifanalysis/Mapper.py to Mapper.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/motifanalysis/Match.py to Match.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/motifanalysis/__init__.py to __init__.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/motifanalysis/Statistics.py to Statistics.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/motifanalysis/Util.py to Util.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/motifanalysis/Main.py to Main.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/motifanalysis/Enrichment.py to Enrichment.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/motifanalysis/Motif.py to Motif.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/__version__.py to __version__.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/helper.py to helper.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/viz/lineplot.py to lineplot.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/viz/__init__.py to __init__.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/viz/combinatorial_test.py to combinatorial_test.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/viz/shared_function.py to shared_function.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/viz/Main.py to Main.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/viz/boxplot.py to boxplot.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/viz/jaccard_test.py to jaccard_test.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/viz/bed_profile.py to bed_profile.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/viz/plotTools.py to plotTools.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/viz/projection_test.py to projection_test.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/viz/intersection_test.py to intersection_test.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/GenomicRegion.py to GenomicRegion.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/GenomicVariantSet.py to GenomicVariantSet.cpython-36.pyc

byte-compiling build/bdist.linux-x86_64/egg/rgt/MotifSet.py to MotifSet.cpython-36.pyc

creating build/bdist.linux-x86_64/egg/EGG-INFO

installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts

running install_scripts

running build_scripts

creating build/scripts-3.6

copying data/bin/linux/bedToBigBed -> build/scripts-3.6

copying data/bin/linux/bigBedToBed -> build/scripts-3.6

copying data/bin/linux/wigToBigWig -> build/scripts-3.6

copying data/bin/linux/bigWigMerge -> build/scripts-3.6

copying data/bin/linux/bedGraphToBigWig -> build/scripts-3.6

creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts

copying build/scripts-3.6/bedGraphToBigWig -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts

copying build/scripts-3.6/bigWigMerge -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts

copying build/scripts-3.6/wigToBigWig -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts

copying build/scripts-3.6/bigBedToBed -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts

copying build/scripts-3.6/bedToBigBed -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts

changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/bedGraphToBigWig to 775

changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/bigWigMerge to 775

changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/wigToBigWig to 775

changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/bigBedToBed to 775

changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/bedToBigBed to 775

copying RGT.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO

copying RGT.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO

copying RGT.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO

copying RGT.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO

copying RGT.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO

copying RGT.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO

zip_safe flag not set; analyzing archive contents...

creating dist

creating 'dist/RGT-0.13.0-py3.6.egg' and adding 'build/bdist.linux-x86_64/egg' to it

removing 'build/bdist.linux-x86_64/egg' (and everything under it)

Processing RGT-0.13.0-py3.6.egg

Copying RGT-0.13.0-py3.6.egg to /home/ubuntu/.local/lib/python3.6/site-packages

Adding RGT 0.13.0 to easy-install.pth file

Traceback (most recent call last):

File "setup.py", line 448, in <module>

platforms=supported_platforms)

File "/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/site-packages/setuptools/__init__.py", line 161, in setup

return distutils.core.setup(**attrs)

File "/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/distutils/core.py", line 148, in setup

dist.run_commands()

File "/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/distutils/dist.py", line 955, in run_commands

self.run_command(cmd)

File "/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/distutils/dist.py", line 974, in run_command

cmd_obj.run()

File "/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/site-packages/setuptools/command/install.py", line 67, in run

self.do_egg_install()

File "/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/site-packages/setuptools/command/install.py", line 117, in do_egg_install

cmd.run(show_deprecation=False)

File "/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 424, in run

self.easy_install(spec, not self.no_deps)

File "/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 673, in easy_install

return self.install_item(None, spec, tmpdir, deps, True)

File "/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 720, in install_item

self.process_distribution(spec, dist, deps)

File "/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 745, in process_distribution

self.install_egg_scripts(dist)

File "/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 619, in install_egg_scripts

dist.get_metadata('scripts/' + script_name)

File "/home/ubuntu/anaconda3/envs/my_env/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1425, in get_metadata

return value.decode('utf-8')

UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa9 in position 25: invalid start byte in scripts/bedGraphToBigWig file at path: /home/ubuntu/.local/lib/python3.6/site-packages/RGT-0.13.0-py3.6.egg/EGG-INFO/scripts/bedGraphToBigWig

ivan....@googlemail.com

unread,

Jul 27, 2020, 12:41:01 PM7/27/20

to RGT Users

Hi all,

I have the same problem of installing RGT: multiple errors in "Building wheel" steps.

Can you please provide some hints? I tried installation in separate conda environment for RGT with pyhton2.7.15.

...

Fabio Ticconi

unread,

Jul 27, 2020, 1:34:39 PM7/27/20

to ivan....@googlemail.com, RGT Users

Hi,

we don't support conda, but this recent message from another user might help:

https://groups.google.com/d/msg/rgtusers/dn97Z3jkV4Q/SkzcSsqjAQAJ

Cheers,

Fabio

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