5 pip install RSeQC安装时候报错,是不是底层的库不全?怎么解决呢

利用教程中的pip install RSeQC,出现三处红色显示的错误,试了下pip install其他的也同样报错,不知道是不是什么库没安装;

分别是bx-python、python-lzo;代码如下,找了好几个版本的答案,没能解决


root@iZbp10cjxe9c7ip0m4hzhwZ:/bioapp# pip install RseQC

Looking in indexes: http://mirrors.cloud.aliyuncs.com/pypi/simple/

Collecting RseQC

  Downloading http://mirrors.cloud.aliyuncs.com/pypi/packages/ad/2d/b522357135fbaebcd34e57183045107b87015155542ff4b84e73f95f69a2/RSeQC-2.6.4-py2-none-any.whl (130kB)

    100% |████████████████████████████████| 133kB 15.6MB/s 

Requirement already satisfied: cython>=0.17 in /usr/local/lib/python2.7/dist-packages (from RseQC) (0.28.4)

Requirement already satisfied: pysam in /usr/local/lib/python2.7/dist-packages (from RseQC) (0.14.1)

Collecting bx-python (from RseQC)

  Downloading http://mirrors.cloud.aliyuncs.com/pypi/packages/74/3e/f19be7f3fb6c6f7d4932050e3dfb1634354c6e896e27d2301ba4df9145e0/bx-python-0.8.1.tar.gz (1.3MB)

    100% |████████████████████████████████| 1.3MB 27.4MB/s 

Collecting numpy (from RseQC)

  Downloading http://mirrors.cloud.aliyuncs.com/pypi/packages/6a/a9/c01a2d5f7b045f508c8cefef3b079fe8c413d05498ca0ae877cffa230564/numpy-1.14.5-cp27-cp27mu-manylinux1_x86_64.whl (12.1MB)

    100% |████████████████████████████████| 12.1MB 31.1MB/s 

Collecting python-lzo (from bx-python->RseQC)

  Downloading http://mirrors.cloud.aliyuncs.com/pypi/packages/af/60/41f17f56c920a956f1d4b9f04f9755c045b2b06b9dd933b33cdd37ab9fd7/python-lzo-1.12.tar.gz

Requirement already satisfied: six in /usr/local/lib/python2.7/dist-packages (from bx-python->RseQC) (1.11.0)

Building wheels for collected packages: bx-python, python-lzo

  Running setup.py bdist_wheel for bx-python ... error

  Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-ZbI2FB/bx-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-iavnDe --python-tag cp27:

  Traceback (most recent call last):

    File "<string>", line 1, in <module>

    File "/tmp/pip-install-ZbI2FB/bx-python/setup.py", line 266, in <module>

      main()

    File "/tmp/pip-install-ZbI2FB/bx-python/setup.py", line 73, in main

      raise Exception( "numpy must be installed to build" )

  Exception: numpy must be installed to build

  

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

  Failed building wheel for bx-python

  Running setup.py clean for bx-python

  Running setup.py bdist_wheel for python-lzo ... error

  Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-ZbI2FB/python-lzo/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-z6DPys --python-tag cp27:

  running bdist_wheel

  running build

  running build_ext

  building 'lzo' extension

  creating build

  creating build/temp.linux-x86_64-2.7

  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/usr/include/lzo -I/usr/include/python2.7 -c lzomodule.c -o build/temp.linux-x86_64-2.7/lzomodule.o

  lzomodule.c:35:23: fatal error: lzo/lzo1x.h: No such file or directory

  compilation terminated.

  error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

  

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

  Failed building wheel for python-lzo

  Running setup.py clean for python-lzo

Failed to build bx-python python-lzo

Installing collected packages: python-lzo, numpy, bx-python, RseQC

  Running setup.py install for python-lzo ... error

    Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-ZbI2FB/python-lzo/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-RR2UTz/install-record.txt --single-version-externally-managed --compile:

    running install

    running build

    running build_ext

    building 'lzo' extension

    creating build

    creating build/temp.linux-x86_64-2.7

    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/usr/include/lzo -I/usr/include/python2.7 -c lzomodule.c -o build/temp.linux-x86_64-2.7/lzomodule.o

    lzomodule.c:35:23: fatal error: lzo/lzo1x.h: No such file or directory

    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-install-ZbI2FB/python-lzo/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-RR2UTz/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-ZbI2FB/python-lzo/

You are using pip version 10.0.1, however version 18.0 is available.

You should consider upgrading via the 'pip install --upgrade pip' command.


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最佳答案 2018-07-25 13:12

##RSeQC的安装

pip install numpy

在https://omictools.com/bx-python-tool网站下载bx-python-0.8.1.tar.gz

tar -zxvf bx-python-0.8.1.tar.gz

cd bx-python-0.8.1

python setup.py install

cd /bioapp/

sudo apt-get install liblzo2-dev

pip install RSeQC

***************************************

即可成功

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其它 2 个回答

omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

最后一个错误有问题,GCC编译出错,你的系统环境不清楚,建议Google一下错误原因。

有时候也贴一下错误文字,方便别人帮你搜索一下。


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海阔天空

关于pip install RSeQC的安装

我已经按照上边答案中说明做了,但是为什么还是不能成功呢。attachments-2019-01-JU0qOe2E5c3ae8d0a33f3.jpg

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  • Ideal 提出于 2018-07-24 10:17