How Troubleshoot Failed Installation of pywfdb from pip?

Question

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 do sudo -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 gives pywfdb (0.1.1) - Python interface to WFDB library so I expect it to include also the module which you can import.
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. Command ls /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 and ls /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)

Can you get the package if you install it inside a virtualenv? In a virtualenv you're free from ubuntu's package manager. Also find /usr/local/lib/python2.7/dist-packages -name '*wfdb*' should be more effective than plain ls — grochmal, Jul 10 '16 at 17:18
Well, if tests do not pass in setup.py it will not install the module. Pyrex is a wrapper for C code, and the underlying wfdb library is in C code, therefore i suspect you do not have wfdb installed. — grochmal, Jul 10 '16 at 17:34
You can follow either the installation guide provided by pywfdb or the one provided by wfdb itself — grochmal, Jul 10 '16 at 17:37
@Masi Try sudo apt install python-pyrex and then sudo -H pip install pywfdb and see if that resolves the ImportError. — edwinksl, Jul 10 '16 at 17:39
Stop ignoring errors! You created a snowball of errors that you cannot get out off. Your first problem is that there is something wrong with upstart. Fix that first, then update apt-get as far as you can and test if it works, only then go for installing new stuff. — grochmal, Jul 10 '16 at 17:53
You need a running dpkg, without a running dpkg/apt-get your system is neigh useless. And i mean the part about "ignoring errors" until you have Pyrex and wfdb you will not be able to install pywfdb. Errors must be fixed bottom up, otherwise they will keep biting. — grochmal, Jul 10 '16 at 18:05
Fair enough, it is worth a try. You can setup a virtualenv and install Pyrex and then try pywfdb (I assume you are 100% you have the wfdb 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 fix dpkg. Also, ul.SE will suggest in a moment to move this to /dev/chat. — grochmal, Jul 10 '16 at 20:19

score 1 · Answer 1 · edited Apr 06 '19 at 00:58

Masi,

finally I could run this library. My steps are as follows:

download wfdb-10.5.24 from physionet website
compile and install

cd /usr/include
sudo ln -s /usr/local/include/wfdb wfdb

sudo apt-get install python-pyrex
open this file by any text editor pywfdb/_pywfdb.c and replace these lines into:
```
#include <wfdb/ecgcodes.h>
#include <wfdb/ecgmap.h>
#include <wfdb/wfdb.h>
```
in setup.py file on lines 14 and 15 put the path of wfdb-10.5.24/lib directory
python setup.py install

Linux: Ubuntu 16.04

Monstah · Accepted Answer · 2016-09-01T02:26:46.790

Expanding on the above answer, since it pointed me in the right direction but skipped a few keysteps.

Disclaimer: I am not an experienced Linux user, but this worked on a clean DigitalOcean Ubuntu install.

depencies (in case you haven't already):
- $ sudo apt-get install python-dev python-pip python-pyrex unzip
download WFDB source from www.physionet.org/physiotools/wfdb.tar.gz
- extract to ~/
Compile and install the WFDB C library
- @~/wfdb-10.5.24/wfdb$ ./configure --without-netfiles --static --static_only
- (the tutorial at http://www.pybytes.com/pywfdb/ says you need to use --without-netfiles switch; ~~i didn't have any problems by not using it, but couldn't get the python wrapper to import from physionet~~ and so you should)
- @~/wfdb-10.5.24/wfdb$ sudo make install
- @~/wfdb-10.5.24/wfdb$ make check
download pywfdb source from pypi.python.org/packages/source/p/pywfdb/pywfdb-0.1.1.zip
- unzip to ~/
edit ~/pywfdb-0.1.1/pywfdb/_pywfdb.c
- replace \*.h with <wfdb/*.h> in lines 15, 16, 17
edit ~/pywfdb-0.1.1/setup.py
- replace ./wfdb-10.4.4/ with /home/username/wfdb-10.5.24/ in lines 14, 15 (or wherever you extracted it to; the ~/ alias did not work for me)
@/usr/include$ ln -s /usr/local/include/wfdb wfdb
@~/pywfdb$ sudo python setup.py install
(above answer ends here, but I needed this extra step to actually import the lib within python) @/usr/lib/python2.7/dist-packages$ ln -s /usr/local/lib/python2.7/dist-packages/pywfdb pywfdb

It would be great if you can also include xenith's proposal in your answer as one solution. I really like your answer. — Léo Léopold Hertz 준영, Aug 31 '16 at 20:18

How Troubleshoot Failed Installation of pywfdb from pip?

Troubleshooting Methods

2 Answers2