gmstanle
commented
4 years ago I get a similar error. I am installing on Linux (Ubuntu 16.04) in a conda environment with Python=3.7.6 and pip=20.0.2 using pip install HTSeq. I think it has something to do with the gnu c compiler but I'm not sure exactly what it is.
Collecting HTSeq
Downloading HTSeq-0.11.2.tar.gz (611 kB)
|████████████████████████████████| 611 kB 20.6 MB/s
Requirement already satisfied: numpy in /home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/lib/python3.7/site-packages (from HTSeq) (1.17.5)
Requirement already satisfied: pysam>=0.9.0 in /home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/lib/python3.7/site-packages (from HTSeq) (0.15.4)
Building wheels for collected packages: HTSeq
Building wheel for HTSeq (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-iojgnko6/HTSeq/setup.py'"'"'; __file__='"'"'/tmp/pip-install-iojgnko6/HTSeq/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-9ncn_z5n
cwd: /tmp/pip-install-iojgnko6/HTSeq/
Complete output (98 lines):
symlinking folders for python3
running bdist_wheel
running build
running build_py
running preprocess
cythonizing
Cython version 0.23.4
SWIGging
correcting SWIG for python3
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: No changes to python3/src/StepVector.py
RefactoringTool: Files that need to be modified:
RefactoringTool: python3/src/StepVector.py
moving swigged .py module
done
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/HTSeq
copying HTSeq/__init__.py -> build/lib.linux-x86_64-3.7/HTSeq
copying HTSeq/_HTSeq_internal.py -> build/lib.linux-x86_64-3.7/HTSeq
copying HTSeq/StepVector.py -> build/lib.linux-x86_64-3.7/HTSeq
copying HTSeq/_version.py -> build/lib.linux-x86_64-3.7/HTSeq
creating build/lib.linux-x86_64-3.7/HTSeq/scripts
copying HTSeq/scripts/__init__.py -> build/lib.linux-x86_64-3.7/HTSeq/scripts
copying HTSeq/scripts/qa.py -> build/lib.linux-x86_64-3.7/HTSeq/scripts
copying HTSeq/scripts/count.py -> build/lib.linux-x86_64-3.7/HTSeq/scripts
running build_ext
building 'HTSeq._HTSeq' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/src
/home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/include -fPIC -I/home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/lib/python3.7/site-packages/numpy/core/include -I/home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/include/python3.7m -c src/_HTSeq.c -o build/temp.linux-x86_64-3.7/src/_HTSeq.o -w
src/_HTSeq.c: In function '__Pyx_ExceptionSave':
src/_HTSeq.c:44420:21: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
*type = tstate->exc_type;
^~~~~~~~
curexc_type
src/_HTSeq.c:44421:22: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
*value = tstate->exc_value;
^~~~~~~~~
curexc_value
src/_HTSeq.c:44422:19: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
*tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
src/_HTSeq.c: In function '__Pyx_ExceptionReset':
src/_HTSeq.c:44434:24: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
tmp_type = tstate->exc_type;
^~~~~~~~
curexc_type
src/_HTSeq.c:44435:25: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
src/_HTSeq.c:44436:22: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
src/_HTSeq.c:44437:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
tstate->exc_type = type;
^~~~~~~~
curexc_type
src/_HTSeq.c:44438:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
tstate->exc_value = value;
^~~~~~~~~
curexc_value
src/_HTSeq.c:44439:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
tstate->exc_traceback = tb;
^~~~~~~~~~~~~
curexc_traceback
src/_HTSeq.c: In function '__Pyx_GetException':
src/_HTSeq.c:44482:24: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
tmp_type = tstate->exc_type;
^~~~~~~~
curexc_type
src/_HTSeq.c:44483:25: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
src/_HTSeq.c:44484:22: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
src/_HTSeq.c:44485:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
tstate->exc_type = local_type;
^~~~~~~~
curexc_type
src/_HTSeq.c:44486:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
tstate->exc_value = local_value;
^~~~~~~~~
curexc_value
src/_HTSeq.c:44487:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
tstate->exc_traceback = local_tb;
^~~~~~~~~~~~~
curexc_traceback
error: command '/home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/bin/x86_64-conda_cos6-linux-gnu-cc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for HTSeq
Running setup.py clean for HTSeq
Failed to build HTSeq
Installing collected packages: HTSeq
Running setup.py install for HTSeq ... error
ERROR: Command errored out with exit status 1:
command: /home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-iojgnko6/HTSeq/setup.py'"'"'; __file__='"'"'/tmp/pip-install-iojgnko6/HTSeq/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-cu6z1f_s/install-record.txt --single-version-externally-managed --compile --install-headers /home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/include/python3.7m/HTSeq
cwd: /tmp/pip-install-iojgnko6/HTSeq/
Complete output (98 lines):
symlinking folders for python3
running install
running build
running build_py
running preprocess
cythonizing
Cython version 0.23.4
SWIGging
correcting SWIG for python3
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: No changes to python3/src/StepVector.py
RefactoringTool: Files that need to be modified:
RefactoringTool: python3/src/StepVector.py
moving swigged .py module
done
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/HTSeq
copying HTSeq/__init__.py -> build/lib.linux-x86_64-3.7/HTSeq
copying HTSeq/_HTSeq_internal.py -> build/lib.linux-x86_64-3.7/HTSeq
copying HTSeq/StepVector.py -> build/lib.linux-x86_64-3.7/HTSeq
copying HTSeq/_version.py -> build/lib.linux-x86_64-3.7/HTSeq
creating build/lib.linux-x86_64-3.7/HTSeq/scripts
copying HTSeq/scripts/__init__.py -> build/lib.linux-x86_64-3.7/HTSeq/scripts
copying HTSeq/scripts/qa.py -> build/lib.linux-x86_64-3.7/HTSeq/scripts
copying HTSeq/scripts/count.py -> build/lib.linux-x86_64-3.7/HTSeq/scripts
running build_ext
building 'HTSeq._HTSeq' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/src
/home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/include -fPIC -I/home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/lib/python3.7/site-packages/numpy/core/include -I/home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/include/python3.7m -c src/_HTSeq.c -o build/temp.linux-x86_64-3.7/src/_HTSeq.o -w
src/_HTSeq.c: In function '__Pyx_ExceptionSave':
src/_HTSeq.c:44420:21: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
*type = tstate->exc_type;
^~~~~~~~
curexc_type
src/_HTSeq.c:44421:22: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
*value = tstate->exc_value;
^~~~~~~~~
curexc_value
src/_HTSeq.c:44422:19: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
*tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
src/_HTSeq.c: In function '__Pyx_ExceptionReset':
src/_HTSeq.c:44434:24: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
tmp_type = tstate->exc_type;
^~~~~~~~
curexc_type
src/_HTSeq.c:44435:25: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
src/_HTSeq.c:44436:22: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
src/_HTSeq.c:44437:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
tstate->exc_type = type;
^~~~~~~~
curexc_type
src/_HTSeq.c:44438:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
tstate->exc_value = value;
^~~~~~~~~
curexc_value
src/_HTSeq.c:44439:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
tstate->exc_traceback = tb;
^~~~~~~~~~~~~
curexc_traceback
src/_HTSeq.c: In function '__Pyx_GetException':
src/_HTSeq.c:44482:24: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
tmp_type = tstate->exc_type;
^~~~~~~~
curexc_type
src/_HTSeq.c:44483:25: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
src/_HTSeq.c:44484:22: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
src/_HTSeq.c:44485:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
tstate->exc_type = local_type;
^~~~~~~~
curexc_type
src/_HTSeq.c:44486:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
tstate->exc_value = local_value;
^~~~~~~~~
curexc_value
src/_HTSeq.c:44487:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
tstate->exc_traceback = local_tb;
^~~~~~~~~~~~~
curexc_traceback
error: command '/home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/bin/x86_64-conda_cos6-linux-gnu-cc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-iojgnko6/HTSeq/setup.py'"'"'; __file__='"'"'/tmp/pip-install-iojgnko6/HTSeq/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-cu6z1f_s/install-record.txt --single-version-externally-managed --compile --install-headers /home/geoffstanley/anaconda3/envs/pacbio-sc-analysis/include/python3.7m/HTSeq Check the logs for full command output.```
iosonofabio
Hi,
have been trying to install htseq all day and I just can't seem to make it work. I've posted my question on stackoverflow: https://stackoverflow.com/questions/59141485/install-python-htseq-package-in-specific-path-with-apt-get
But for some more context the output when I run pip install, see the attached file. There seems to be some issue with Cython but I just cannot figure out what is missing.
I'd be very gratefull for any help!
output.txt