如何解决从 pip 安装 pywfdb 失败的问题？

Question

条件：无法pywfdb从pip
差异条件中排除库/模块安装失败的故障：pywfdb
排除的依赖项失败：upstart/ Ubuntu 中的systemd设计错误runit这里自 Ubuntu >=14.10
设置

• 小路/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
• PYTHONPATH 中空白$HOME/.bashrc

具有大量日志的依赖项和脏安装的工作流程

• 埃德温克斯尔的建议：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) ...
  - -
  

• 脏安装的工作流程，安装后不进行清理，看看pip要做什么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/
  

打开

• 为什么pywfdb 构建轮子失败？

• 为什么从完整日志中重现以下错误？

  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/
  

故障排除方法

Pip 本地模块，您看不到wfdbAdam 的第一个命令集找到的内容

" 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']

包/模块/库信息的测试命令不成功

• pip search wfdb给出pywfdb (0.1.1) - Python interface to WFDB library，所以我希望它还包括您可以使用的模块import。
• find /usr/local/lib/python2.7/dist-packages -name '*wfdb*'返回空白。
• pip list |grep wfdb返回空白。
• pip show pywfdb返回空白。

测试代码显示未找到该模块

" http://www.pybytes.com/pywfdb/ "
import pywfdb

尝试搜索模块

• 没有像普通的 python 包一样安装，因为不是/usr/lib/python<version>/site-packages按照描述的那样安装的这里;我搜索了所有目录（/usr/local/lib/python2.7/和/usr/local/lib/python3.5/）。

• 不是dist-packages基于回答。命令ls /usr/local/lib/python2.7/dist-packages/ | grep wfdb返回空白。

• >>> import site; site.getsitepackages()给出输出

  ['/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages']
  

  ls /usr/local/lib/python2.7/dist-packages | grep wfdb和 的空白输出ls /usr/lib/python2.7/dist-packages | grep wfdb。

系统：Linux Ubuntu 16.04 64 位
Linux 内核：4.6
Linux 内核选项：wl
硬件：Macbook Air 2013-mid
Python：2.7.11+
Pip：最新 (8.1.2)pip install --upgrade pip返回Requirement already up-to-date: pip in /home/masi/.local/lib/python2.7/site-packages
最新 pip模块：在 Bashpip freeze --local | grep -v '^\-e' | cut -d = -f 1 | xargs -n1 pip install -U之前完成
：4.3.46(1)-release (x86_64-pc-linux-gnu)

Answer 1

扩展上述答案，因为它为我指明了正确的方向，但跳过了一些关键步骤。

免责声明：我不是一个经验丰富的 Linux 用户，但这适用于干净的 DigitalOcean Ubuntu 安装。

1. 依赖项（如果你还没有）：

   • $ sudo apt-get install python-dev python-pip python-pyrex unzip

2. 从以下位置下载 WFDB 源代码www.physionet.org/physiotools/wfdb.tar.gz

   • 解压到~/

3. 编译并安装 WFDB C 库

   • @~/wfdb-10.5.24/wfdb$ ./configure --without-netfiles --static --static_only
   • （教程位于http://www.pybytes.com/pywfdb/说你需要使用--without-netfiles开关；我没有遇到任何问题不是使用它，但无法从 phyonet 导入 python 包装器，所以你应该）
   • @~/wfdb-10.5.24/wfdb$ sudo make install
   • @~/wfdb-10.5.24/wfdb$ make check

4. 从下载 pywfdb 源pypi.python.org/packages/source/p/pywfdb/pywfdb-0.1.1.zip

   • 解压到~/

5. 编辑~/pywfdb-0.1.1/pywfdb/_pywfdb.c

   • 替换\*.h为<wfdb/*.h>第 15、16、17 行

6. 编辑~/pywfdb-0.1.1/setup.py

   • 在第 14、15 行中替换./wfdb-10.4.4/为（或将其提取到的任何位置；别名对我不起作用）/home/username/wfdb-10.5.24/~/

7. @/usr/include$ ln -s /usr/local/include/wfdb wfdb

8. @~/pywfdb$ sudo python setup.py install

9. （上面的答案到此结束，但我需要这个额外的步骤来实际导入 python 中的库）@/usr/lib/python2.7/dist-packages$ ln -s /usr/local/lib/python2.7/dist-packages/pywfdb pywfdb

Answer 2

马西，

我终于可以运行这个库了。我的步骤如下：

1. wfdb-10.5.24从 phyonet 网站下载
2. 编译并安装

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

4. sudo apt-get install python-pyrex

5. 使用任何文本编辑器打开此文件pywfdb/_pywfdb.c并将这些行替换为：

   #include <wfdb/ecgcodes.h>
   #include <wfdb/ecgmap.h>
   #include <wfdb/wfdb.h>
   

6. 在第 14 行和第 15 行的文件中放置目录setup.py路径wfdb-10.5.24/lib

7. python setup.py install

Linux：Ubuntu 16.04