paddlehelix安装问题 #273
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[你好pal，根据此链接(https://blog.csdn.net/Go_ahead_forever/article/details/133755918)的第3个方法，在Linux上设置环境变量可以解决sklearn改名的问题] |
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您好，
非常感激收到您的来信，感谢您的解答。之前看错误打印时第三种方法：
as a last resort, set the environment variable SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True to avoid this error
就是您提到的解决方案。
但是我希望能在windows系统下运行该框架，不知道怎么在windows下实现方法3的设置环境变量，这部分您是否了解呢？还有就是下载的源里面的requirements.txt文件我怎么可以更改呢？
非常期待得到您的回复，不胜感激！祝工作顺利，万事如意！
完整打印：（执行“pip install paddlehelix”）
Looking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple
Collecting paddlehelix
Using cached https://pypi.tuna.tsinghua.edu.cn/packages/ee/57/23cfeb5860e57a69610136dfc34826ce8c10693766d6db777cc3ff1711b1/paddlehelix-1.0.1-cp37-cp37m-win_amd64.whl (210 kB)
Requirement already satisfied: numpy in e:\anaconda3\envs\paddlehelix\lib\site-packages (from paddlehelix) (1.21.6)
Requirement already satisfied: pandas in e:\anaconda3\envs\paddlehelix\lib\site-packages (from paddlehelix) (1.3.5)
Collecting networkx (from paddlehelix)
Using cached https://pypi.tuna.tsinghua.edu.cn/packages/e9/93/aa6613aa70d6eb4868e667068b5a11feca9645498fd31b954b6c4bb82fa5/networkx-2.6.3-py3-none-any.whl (1.9 MB)
Collecting sklearn (from paddlehelix)
Downloading https://pypi.tuna.tsinghua.edu.cn/packages/46/1c/395a83ee7b2d2ad7a05b453872053d41449564477c81dc356f720b16eac4/sklearn-0.0.post12.tar.gz (2.6 kB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [15 lines of output]
The 'sklearn' PyPI package is deprecated, use 'scikit-learn'
rather than 'sklearn' for pip commands.
Here is how to fix this error in the main use cases:
- use 'pip install scikit-learn' rather than 'pip install sklearn'
- replace 'sklearn' by 'scikit-learn' in your pip requirements files
(requirements.txt, setup.py, setup.cfg, Pipfile, etc ...)
- if the 'sklearn' package is used by one of your dependencies,
it would be great if you take some time to track which package uses
'sklearn' instead of 'scikit-learn' and report it to their issue tracker
- as a last resort, set the environment variable
SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True to avoid this error
More information is available at
https://github.com/scikit-learn/sklearn-pypi-package
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
…------------------ 原始邮件 ------------------
发件人: "PaddlePaddle/PaddleHelix" ***@***.***>;
发送时间: 2023年12月3日(星期天) 晚上7:15
***@***.***>;
抄送: "Shaun ***@***.******@***.***>;
主题: Re: [PaddlePaddle/PaddleHelix] paddlehelix安装问题 (Issue #273)
[你好pal，根据此链接(https://blog.csdn.net/Go_ahead_forever/article/details/133755918)的第3个方法，在Linux上设置环境变量可以解决sklearn改名的问题]
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您好，我后面查到了windows的相关操作，即set；非常感激您的帮助，谢谢！
…------------------ 原始邮件 ------------------
发件人: "PaddlePaddle/PaddleHelix" ***@***.***>;
发送时间: 2023年12月3日(星期天) 晚上7:15
***@***.***>;
抄送: "Shaun ***@***.******@***.***>;
主题: Re: [PaddlePaddle/PaddleHelix] paddlehelix安装问题 (Issue #273)
[你好pal，根据此链接(https://blog.csdn.net/Go_ahead_forever/article/details/133755918)的第3个方法，在Linux上设置环境变量可以解决sklearn改名的问题]
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您好，我根据网站(https://gitee.com/paddle-helix/PaddleHelix/blob/dev/installation_guide_cn.md)的指导步骤去安装项目，现已解决问题安装完了，但是在运行案例时出了错（参考附件和文末的打印内容）。
我不太明白paddlehelix安装后paddle和它的关系，我之前没像链接里面在conda安装，而是直接在pycharm上运行也出现和它相关的错误，跟着网上也试过很多种方法，但一直也解决不了。
安装requirement.txt也出现报错，但是好像只是和已安装出现冲突。
非常感谢您的收看，也非常希望得到您的解答，万分感谢！
***@***.***
具体打印：
(paddlehelix) E:\ACEDesktop\药物靶标亲和力预测\PaddleHelix-dev\apps\drug_target_interaction\moltrans_dti>set CUDA_VISIBLE_DEVICES=0
(paddlehelix) E:\ACEDesktop\药物靶标亲和力预测\PaddleHelix-dev\apps\drug_target_interaction\moltrans_dti>python train_cls.py --batchsize 64 --epochs 200 --lr 5e-4 --dataset cls_davis
Traceback (most recent call last):
File "train_cls.py", line 18, in <module>
from helper import utils
File "E:\ACEDesktop\药物靶标亲和力预测\PaddleHelix-dev\apps\drug_target_interaction\moltrans_dti\helper\utils\__init__.py", line 23, in <module>
from .paddle_varbase import *
File "E:\ACEDesktop\药物靶标亲和力预测\PaddleHelix-dev\apps\drug_target_interaction\moltrans_dti\helper\utils\paddle_varbase.py", line 21, in <module>
VarBase.tmp = VarBase.__getitem__
…--------------------------------------------------------------------------------------------------------------------------------------------
Requirement already satisfied: protobuf>=3.1.0 in e:\anaconda3\envs\paddlehelix\lib\site-packages (from paddlepaddle==2.0.2->-r requirement.txt (line 1)) (3.20.2)
Requirement already satisfied: Pillow in e:\anaconda3\envs\paddlehelix\lib\site-packages (from paddlepaddle==2.0.2->-r requirement.txt (line 1)) (9.2.0)
Requirement already satisfied: six in e:\anaconda3\envs\paddlehelix\lib\site-packages (from paddlepaddle==2.0.2->-r requirement.txt (line 1)) (1.16.0)
Requirement already satisfied: decorator in e:\anaconda3\envs\paddlehelix\lib\site-packages (from paddlepaddle==2.0.2->-r requirement.txt (line 1)) (5.1.1)
Requirement already satisfied: astor in e:\anaconda3\envs\paddlehelix\lib\site-packages (from paddlepaddle==2.0.2->-r requirement.txt (line 1)) (0.8.1)
Collecting gast==0.3.3 (from paddlepaddle==2.0.2->-r requirement.txt (line 1))
Downloading https://pypi.tuna.tsinghua.edu.cn/packages/d6/84/759f5dd23fec8ba71952d97bcc7e2c9d7d63bdc582421f3cd4be845f0c98/gast-0.3.3-py2.py3-none-any.whl (9.7 kB)
INFO: pip is looking at multiple versions of paddlepaddle to determine which version is compatible with other requirements. This could take a while.
ERROR: Cannot install -r requirement.txt (line 1) and numpy==1.19.5 because these package versions have conflicting dependencies.
The conflict is caused by:
The user requested numpy==1.19.5
paddlepaddle 2.0.2 depends on numpy<=1.19.3 and >=1.13; python_version >= "3.5" and platform_system == "Windows"
To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict
ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts
------------------ 原始邮件 ------------------
发件人: "PaddlePaddle/PaddleHelix" ***@***.***>;
发送时间: 2023年12月3日(星期天) 晚上7:15
***@***.***>;
抄送: "Shaun ***@***.******@***.***>;
主题: Re: [PaddlePaddle/PaddleHelix] paddlehelix安装问题 (Issue #273)
[你好pal，根据此链接(https://blog.csdn.net/Go_ahead_forever/article/details/133755918)的第3个方法，在Linux上设置环境变量可以解决sklearn改名的问题]
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您好，我根据网站(https://gitee.com/paddle-helix/PaddleHelix/blob/dev/installation_guide_cn.md)的指导步骤去安装项目，遇到了一些问题，前面都已经解决，但是最后面安装paddlehelix时出现了问题：
1.用指令pip install paddlehelix安装，它安装的来源是：Looking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple
Collecting paddlehelix
......
Using cached https://pypi.tuna.tsinghua.edu.cn/packages/a4/0b/d1c703256cf293be77b7db44dbef62251fe02a97d0bef981f7120b0b0c0f/sklearn-0.0.post11.tar.gz (3.6 kB)时出现错误提示，主要是说sklearn现在不用了，是用scikit-learn，但是那个网站的东西应该是固定的，我不知道怎么去改它的requirements.txt，所以想了解有没有别的下载源。
2.在github上下载后通过python运行setup.py安装，这里的问题一个是提示：
Please avoid running
setup.pydirectly.Instead, use pypa/build, pypa/installer or other
standards-based tools.
另一个问题是最后有报error：
File "setup.py", line 35, in run
raise RuntimeError(msg)
RuntimeError: CMake missing - probably upgrade to a newer version of Pip?
非常感谢您的收看，也非常希望得到您的解答，万分感谢！
联系邮箱：1090257784@qq.com
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