Condition: unable to troubleshoot failed installation of the library/module pywfdb
from pip
Differential conditions: failed dependenciens of pywfdb
Exclude: upstart
/systemd
design bugs with runit
in Ubuntu here since Ubuntu >=14.10
Settings
- PATH
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
- PYTHONPATH blank in
$HOME/.bashrc
Work flow for dependencies and dirty installation with much logs
Edwinksl's proposal:
sudo apt-get install python-pyrex
Reading package lists... Done Building dependency tree Reading state information... Done The following NEW packages will be installed: python-pyrex 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 2 not fully installed or removed. Need to get 181 kB of archives. After this operation, 996 kB of additional disk space will be used. Get:1 http://archive.ubuntu.com/ubuntu xenial/main amd64 python-pyrex all 0.9.8.5-2.1ubuntu1 [181 kB] Fetched 181 kB in 0s (356 kB/s) Selecting previously unselected package python-pyrex. (Reading database ... 434011 files and directories currently installed.) Preparing to unpack .../python-pyrex_0.9.8.5-2.1ubuntu1_all.deb ... Unpacking python-pyrex (0.9.8.5-2.1ubuntu1) ... Processing triggers for doc-base (0.10.7) ... Processing 1 added doc-base file... Registering documents with scrollkeeper... Processing triggers for man-db (2.7.5-1) ... Setting up runit (2.1.2-3ubuntu1) ... - - Setting up python-pyrex (0.9.8.5-2.1ubuntu1) ... - -
Work flow with dirty installation to not clean up after the install, to see what
pip
was trying to dosudo -H pip install --no-clean pywfdb
Collecting pywfdb Using cached pywfdb-0.1.1.zip Building wheels for collected packages: pywfdb Running setup.py bdist_wheel for pywfdb ... error Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-_Tu9q1/pywfdb/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d /tmp/tmpemnpLdpip-wheel- --python-tag cp27: running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/pywfdb copying pywfdb/__init__.py -> build/lib.linux-x86_64-2.7/pywfdb copying pywfdb/ecgcodes.py -> build/lib.linux-x86_64-2.7/pywfdb package init file 'example/__init__.py' not found (or not a regular file) creating build/lib.linux-x86_64-2.7/pywfdb/example copying example/readinfo.py -> build/lib.linux-x86_64-2.7/pywfdb/example copying example/plot.py -> build/lib.linux-x86_64-2.7/pywfdb/example running build_ext building 'pywfdb._pywfdb' extension creating build/temp.linux-x86_64-2.7 creating build/temp.linux-x86_64-2.7/pywfdb creating build/temp.linux-x86_64-2.7/wfdb-10.4.4 creating build/temp.linux-x86_64-2.7/wfdb-10.4.4/lib x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I./wfdb-10.4.4/lib -I/usr/include/python2.7 -c pywfdb/_pywfdb.c -o build/temp.linux-x86_64-2.7/pywfdb/_pywfdb.o -Wno-uninitialized -Wno-unused pywfdb/_pywfdb.c:15:22: fatal error: ecgcodes.h: No such file or directory #include "ecgcodes.h" ^ compilation terminated. error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 ---------------------------------------- Failed building wheel for pywfdb Running setup.py clean for pywfdb Failed to build pywfdb Installing collected packages: pywfdb Running setup.py install for pywfdb ... error Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-_Tu9q1/pywfdb/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-gdKcwF-record/install-record.txt --single-version-externally-managed --compile: running install running build running build_py creating build creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/pywfdb copying pywfdb/__init__.py -> build/lib.linux-x86_64-2.7/pywfdb copying pywfdb/ecgcodes.py -> build/lib.linux-x86_64-2.7/pywfdb package init file 'example/__init__.py' not found (or not a regular file) creating build/lib.linux-x86_64-2.7/pywfdb/example copying example/readinfo.py -> build/lib.linux-x86_64-2.7/pywfdb/example copying example/plot.py -> build/lib.linux-x86_64-2.7/pywfdb/example running build_ext building 'pywfdb._pywfdb' extension creating build/temp.linux-x86_64-2.7 creating build/temp.linux-x86_64-2.7/pywfdb creating build/temp.linux-x86_64-2.7/wfdb-10.4.4 creating build/temp.linux-x86_64-2.7/wfdb-10.4.4/lib x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I./wfdb-10.4.4/lib -I/usr/include/python2.7 -c pywfdb/_pywfdb.c -o build/temp.linux-x86_64-2.7/pywfdb/_pywfdb.o -Wno-uninitialized -Wno-unused pywfdb/_pywfdb.c:15:22: fatal error: ecgcodes.h: No such file or directory #include "ecgcodes.h" ^ compilation terminated. error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 ---------------------------------------- Command "/usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-_Tu9q1/pywfdb/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-gdKcwF-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-_Tu9q1/pywfdb/
Open
- Why Failed building wheel for pywfdb?
Why the following error reproduced here from the full log?
Command "/usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-_Tu9q1/pywfdb/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-gdKcwF-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-_Tu9q1/pywfdb/
Troubleshooting Methods
Pip local modules where you see no wfdb
found got by Adam's first command set
" https://stackoverflow.com/a/23885252/54964 "
['adium-theme-ubuntu==0.3.4', 'alabaster==0.7.8', 'auxlib==0.0.37', 'babel==2.3.4', 'backports-abc==0.4', 'backports.shutil-get-terminal-size==1.0.0', 'backports.ssl-match-hostname==3.5.0.1', 'beautifulsoup4==4.4.1', 'ccsm==0.9.12.2', 'certifi==2016.2.28', 'chardet==2.3.0', 'compizconfig-python==0.9.12.2', 'configparser==3.5.0', 'cycler==0.10.0', 'decorator==4.0.9', 'docutils==0.12', 'duplicity==0.7.6', 'entrypoints==0.2.2', 'enum34==1.1.6', 'functools32==3.2.3.post2', 'futures==3.0.5', 'html5lib==0.999', 'httplib2==0.9.1', 'imagesize==0.7.1', 'ipykernel==4.3.1', 'ipyparallel==5.0.1', 'ipython-genutils==0.1.0', 'ipython==4.2.0', 'ipywidgets==5.1.5', 'jinja2==2.8', 'jsonschema==2.5.1', 'jupyter-client==4.2.2', 'jupyter-core==4.1.0', 'lockfile==0.12.2', 'lxml==3.5.0', 'markupsafe==0.23', 'matlab-kernel==0.9.6', 'matplotlib==1.5.1', 'metakernel==0.13.0', 'mistune==0.7.2', 'nbconvert==4.2.0', 'nbformat==4.0.1', 'nose==1.3.7', 'notebook==4.2.1', 'numpy==1.11.0', 'pandas==0.18.1', 'path.py==8.2.1', 'pathlib2==2.1.0', 'pdfshuffler==0.6.0', 'pexpect==4.1.0', 'pickleshare==0.7.2', 'pillow==3.1.2', 'pip==8.1.2', 'ptyprocess==0.5.1', 'pycosat==0.6.1', 'pycurl==7.43.0', 'pygments==2.1.3', 'pygobject==3.20.0', 'pyicu==1.9.2', 'pymatbridge==0.5.2', 'pymysql==0.7.2', 'pyparsing==2.1.4', 'pypdf==1.13', 'python-dateutil==2.5.3', 'python-djvulibre==0.7', 'pytz==2016.4', 'pyxdg==0.25', 'pyyaml==3.11', 'pyzmq==15.2.0', 'qtconsole==4.2.1', 'requests==2.10.0', 'scour==0.32', 'setuptools==22.0.5', 'simplegeneric==0.8.1', 'singledispatch==3.4.0.3', 'six==1.10.0', 'snowballstemmer==1.2.1', 'sphinx==1.4.3', 'subprocess32==3.2.6', 'terminado==0.6', 'testpath==0.3', 'tornado==4.3', 'traitlets==4.2.1', 'unity-lens-photos==1.0', 'wheel==0.29.0', 'widgetsnbextension==1.2.3']
Unsuccessful test commands for the info of the package/module/library
pip search wfdb
givespywfdb (0.1.1) - Python interface to WFDB library
so I expect it to include also the module which you canimport
.find /usr/local/lib/python2.7/dist-packages -name '*wfdb*'
returns blank.pip list |grep wfdb
returns blank.pip show pywfdb
returns blank.
Test code which shows that the module is not found
" http://www.pybytes.com/pywfdb/ "
import pywfdb
Trying to search the module
Not installed as normal python package because not in
/usr/lib/python<version>/site-packages
as described here; I searched all directories (/usr/local/lib/python2.7/
and/usr/local/lib/python3.5/
).Not in
dist-packages
based on the answer. Commandls /usr/local/lib/python2.7/dist-packages/ | grep wfdb
returns blank.>>> import site; site.getsitepackages()
gives the output['/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages']
Blank outputs for
ls /usr/local/lib/python2.7/dist-packages | grep wfdb
andls /usr/lib/python2.7/dist-packages | grep wfdb
.
System: Linux Ubuntu 16.04 64 bit
Linux kernel: 4.6
Linux kernel options: wl
Hardware: Macbook Air 2013-mid
Python: 2.7.11+
Pip: latest (8.1.2) pip install --upgrade pip
returns Requirement already up-to-date: pip in /home/masi/.local/lib/python2.7/site-packages
Latest pip modules: pip freeze --local | grep -v '^\-e' | cut -d = -f 1 | xargs -n1 pip install -U
done before
Bash: 4.3.46(1)-release (x86_64-pc-linux-gnu)
virtualenv
? In a virtualenv you're free from ubuntu's package manager. Alsofind /usr/local/lib/python2.7/dist-packages -name '*wfdb*'
should be more effective than plainls
– grochmal Jul 10 '16 at 17:18setup.py
it will not install the module.Pyrex
is a wrapper for C code, and the underlyingwfdb
library is in C code, therefore i suspect you do not havewfdb
installed. – grochmal Jul 10 '16 at 17:34sudo apt install python-pyrex
and thensudo -H pip install pywfdb
and see if that resolves theImportError
. – edwinksl Jul 10 '16 at 17:39apt-get
as far as you can and test if it works, only then go for installing new stuff. – grochmal Jul 10 '16 at 17:53dpkg
, without a runningdpkg
/apt-get
your system is neigh useless. And i mean the part about "ignoring errors" until you havePyrex
andwfdb
you will not be able to installpywfdb
. Errors must be fixed bottom up, otherwise they will keep biting. – grochmal Jul 10 '16 at 18:05virtualenv
and installPyrex
and then trypywfdb
(I assume you are 100% you have thewfdb
lib installed). Yet,Pyrex
must be compiled, if the compiler tree is not OK you're dead in boots and your only option is to fixdpkg
. Also, ul.SE will suggest in a moment to move this to/dev/chat
. – grochmal Jul 10 '16 at 20:19