ubuntu18安装python接口的openslide过程和错误整理 |
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ubuntu18安装python接口的openslide过程和错误整理
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目录
配置安装过程pip直接安装安装openslide依赖：换源继续安装openslide-tools安装python-openslide添加适用于ubuntu版本的PPA安装python-openslidepython降级安装依赖库手动配置依赖库成功安装的方法
配置
包版本python3.6.10pip20.1安装过程
pip直接安装
pip install openslide-python
出现问题： ERROR: Command errored out with exit status 1: command: /media/s2/cyq/anaconda3/envs/keras/bin/python3.6 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-kpd80yg0/openslide-python/setup.py'"'"'; __file__='"'"'/tmp/pip-install-kpd80yg0/openslide-python/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-86l6dxk_ cwd: /tmp/pip-install-kpd80yg0/openslide-python/ Complete output (5 lines): Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-kpd80yg0/openslide-python/setup.py", line 2, in from setuptools import setup, Extension, Feature ImportError: cannot import name 'Feature' ---------------------------------------- ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. 安装openslide依赖： sudo apt install python-opendslide还是一样的问题 试了几种办法都不管用（包括升级python版本，重新搭一个虚拟环境等），最后选择用tar.gz安装 openslide下载网址：OpenSlide 解决办法：降低setuptools版本（原来是46.3.1）pip install setuptools==45 再次安装：python setup.py install --single-version-externally-managed --record /dev/null 出现信息： …… running install_egg_info running egg_info writing openslide_python.egg-info/PKG-INFO writing dependency_links to openslide_python.egg-info/dependency_links.txt writing requirements to openslide_python.egg-info/requires.txt writing top-level names to openslide_python.egg-info/top_level.txt reading manifest file 'openslide_python.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'openslide_python.egg-info/SOURCES.txt' Copying openslide_python.egg-info to /media/s2/cyq/anaconda3/envs/test/lib/python3.8/site-packages/openslide_python-1.1.1-py3.8.egg-info running install_scripts writing list of installed files to '/dev/null'测试，结果报错： (test) cyq@node5-SYS-4029GP-TRT:~/openslide-python-1.1.1$ python Python 3.8.2 | packaged by conda-forge | (default, Apr 24 2020, 08:20:52) [GCC 7.3.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import openslide Traceback (most recent call last): File "", line 1, in File "/media/s2/cyq/openslide-python-1.1.1/openslide/__init__.py", line 29, in from openslide import lowlevel File "/media/s2/cyq/openslide-python-1.1.1/openslide/lowlevel.py", line 58, in _lib = cdll.LoadLibrary('libopenslide.so.0') File "/media/s2/cyq/anaconda3/envs/test/lib/python3.8/ctypes/__init__.py", line 451, in LoadLibrary return self._dlltype(name) File "/media/s2/cyq/anaconda3/envs/test/lib/python3.8/ctypes/__init__.py", line 373, in __init__ self._handle = _dlopen(self._name, mode) OSError: libopenslide.so.0: cannot open shared object file: No such file or directory >>>上网查了说是缺少依赖，需要安装：sudo apt-get install openslide-tools 报错： root@node5-SYS-4029GP-TRT:~# sudo apt-get install openslide-tools Reading package lists... Done Building dependency tree Reading state information... Done The following additional packages will be installed: libopenjp2-7 libopenslide0 Suggested packages: libtiff-tools The following NEW packages will be installed: libopenjp2-7 libopenslide0 openslide-tools 0 upgraded, 3 newly installed, 0 to remove and 201 not upgraded. Need to get 141 kB/237 kB of archives. After this operation, 696 kB of additional disk space will be used. Do you want to continue? [Y/n] Y Ign:1 http://cn.archive.ubuntu.com/ubuntu disco-updates/universe amd64 libopenjp2-7 amd64 2.3.0-2build0.19.04.1 Err:1 http://security.ubuntu.com/ubuntu disco-updates/universe amd64 libopenjp2-7 amd64 2.3.0-2build0.19.04.1 404 Not Found [IP: 91.189.91.39 80] E: Failed to fetch http://security.ubuntu.com/ubuntu/pool/universe/o/openjpeg2/libopenjp2-7_2.3.0-2build0.19.04.1_amd64.deb 404 Not Found [IP: 91.189.91.39 80] E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?按照提示：apt-get update 报错： root@node5-SYS-4029GP-TRT:~# apt-get update Ign:1 http://cn.archive.ubuntu.com/ubuntu disco InRelease Ign:2 http://security.ubuntu.com/ubuntu disco-security InRelease Ign:3 http://cn.archive.ubuntu.com/ubuntu disco-updates InRelease Hit:4 http://ppa.launchpad.net/graphics-drivers/ppa/ubuntu disco InRelease Err:5 http://security.ubuntu.com/ubuntu disco-security Release 404 Not Found [IP: 91.189.88.152 80] Ign:6 http://cn.archive.ubuntu.com/ubuntu disco-backports InRelease Err:7 http://cn.archive.ubuntu.com/ubuntu disco Release 404 Not Found [IP: 91.189.91.39 80] Err:8 http://cn.archive.ubuntu.com/ubuntu disco-updates Release 404 Not Found [IP: 91.189.91.39 80] Err:9 http://cn.archive.ubuntu.com/ubuntu disco-backports Release 404 Not Found [IP: 91.189.91.39 80] Reading package lists... Done E: The repository 'http://security.ubuntu.com/ubuntu disco-security Release' no longer has a Release file. N: Updating from such a repository can't be done securely, and is therefore disabled by default. N: See apt-secure(8) manpage for repository creation and user configuration details. E: The repository 'http://cn.archive.ubuntu.com/ubuntu disco Release' no longer has a Release file. N: Updating from such a repository can't be done securely, and is therefore disabled by default. N: See apt-secure(8) manpage for repository creation and user configuration details. E: The repository 'http://cn.archive.ubuntu.com/ubuntu disco-updates Release' no longer has a Release file. N: Updating from such a repository can't be done securely, and is therefore disabled by default. N: See apt-secure(8) manpage for repository creation and user configuration details. E: The repository 'http://cn.archive.ubuntu.com/ubuntu disco-backports Release' no longer has a Release file. N: Updating from such a repository can't be done securely, and is therefore disabled by default. N: See apt-secure(8) manpage for repository creation and user configuration details. 换源 获取权限：sudo su进入文件夹cd /etc/apt/备份源：cp sources.list sources.list.bk打开文件sources.list：vim sources.list换源1： 将文件内的内容改为：deb http://cn.archive.ubuntu.com/ubuntu/ xenial main restricted universe multiverse deb http://cn.archive.ubuntu.com/ubuntu/ xenial-security main restricted universe multiverse deb http://cn.archive.ubuntu.com/ubuntu/ xenial-updates main restricted universe multiverse deb http://cn.archive.ubuntu.com/ubuntu/ xenial-backports main restricted universe multiverse ##测试版源 deb http://cn.archive.ubuntu.com/ubuntu/ xenial-proposed main restricted universe multiverse # 源码 deb-src http://cn.archive.ubuntu.com/ubuntu/ xenial main restricted universe multiverse deb-src http://cn.archive.ubuntu.com/ubuntu/ xenial-security main restricted universe multiverse deb-src http://cn.archive.ubuntu.com/ubuntu/ xenial-updates main restricted universe multiverse deb-src http://cn.archive.ubuntu.com/ubuntu/ xenial-backports main restricted universe multiverse ##测试版源 deb-src http://cn.archive.ubuntu.com/ubuntu/ xenial-proposed main restricted universe multiverse注：没有用清华源，是一个不知道什么的源 继续安装openslide-tools指令sudo apt-get install openslide-tools 报错： root@node5-SYS-4029GP-TRT:/etc/apt# sudo apt-get install openslide-tools Reading package lists... Done Building dependency tree Reading state information... Done The following additional packages will be installed: libopenjpeg5 libopenslide0 libpng12-0 Suggested packages: libtiff-tools The following NEW packages will be installed: libopenjpeg5 libopenslide0 libpng12-0 openslide-tools 0 upgraded, 4 newly installed, 0 to remove and 40 not upgraded. Need to get 305 kB of archives. After this operation, 1,098 kB of additional disk space will be used. Do you want to continue? [Y/n] Y Get:1 http://cn.archive.ubuntu.com/ubuntu xenial/universe amd64 libopenjpeg5 amd64 1:1.5.2-3.1 [104 kB] Get:2 http://cn.archive.ubuntu.com/ubuntu xenial-security/main amd64 libpng12-0 amd64 1.2.54-1ubuntu1.1 [116 kB] Get:3 http://cn.archive.ubuntu.com/ubuntu xenial/universe amd64 libopenslide0 amd64 3.4.0-1build1 [70.9 kB] Get:4 http://cn.archive.ubuntu.com/ubuntu xenial/universe amd64 openslide-tools amd64 3.4.0-1build1 [13.9 kB] Fetched 305 kB in 3s (121 kB/s) Selecting previously unselected package libopenjpeg5:amd64. (Reading database ... 215346 files and directories currently installed.) Preparing to unpack .../libopenjpeg5_1%3a1.5.2-3.1_amd64.deb ... Unpacking libopenjpeg5:amd64 (1:1.5.2-3.1) ... Selecting previously unselected package libpng12-0:amd64. Preparing to unpack .../libpng12-0_1.2.54-1ubuntu1.1_amd64.deb ... Unpacking libpng12-0:amd64 (1.2.54-1ubuntu1.1) ... dpkg: error processing archive /var/cache/apt/archives/libpng12-0_1.2.54-1ubuntu1.1_amd64.deb (--unpack): unable to install new version of '/lib/x86_64-linux-gnu/libpng12.so.0': No such file or directory No apport report written because the error message indicates an issue on the local system Selecting previously unselected package libopenslide0. Preparing to unpack .../libopenslide0_3.4.0-1build1_amd64.deb ... Unpacking libopenslide0 (3.4.0-1build1) ... Selecting previously unselected package openslide-tools. Preparing to unpack .../openslide-tools_3.4.0-1build1_amd64.deb ... Unpacking openslide-tools (3.4.0-1build1) ... Errors were encountered while processing: /var/cache/apt/archives/libpng12-0_1.2.54-1ubuntu1.1_amd64.deb E: Sub-process /usr/bin/dpkg returned an error code (1) 安装python-openslidesudo apt-get install python openslide 报错： root@node5-SYS-4029GP-TRT:/media/s2/cyq# sudo apt-get install python-openslide Reading package lists... Done Building dependency tree Reading state information... Done You might want to run 'apt --fix-broken install' to correct these. The following packages have unmet dependencies: libopenslide0 : Depends: libpng12-0 (>= 1.2.13-4) but it is not going to be installed openslide-tools : Depends: libpng12-0 (>= 1.2.13-4) but it is not going to be installed python-openslide : Depends: python (< 2.8) but it is not going to be installed Depends: python (>= 2.7~) but it is not going to be installed Depends: python-pil but it is not going to be installed Depends: python:any (>= 2.7.5-5~) Recommends: python-openslide-examples but it is not going to be installed E: Unmet dependencies. Try 'apt --fix-broken install' with no packages (or specify a solution).根据指令apt --fix-broken install 报错： root@node5-SYS-4029GP-TRT:/media/s2/cyq# apt --fix-broken install Reading package lists... Done Building dependency tree Reading state information... Done Correcting dependencies... Done The following additional packages will be installed: libpng12-0 The following NEW packages will be installed: libpng12-0 0 upgraded, 1 newly installed, 0 to remove and 40 not upgraded. 3 not fully installed or removed. Need to get 0 B/116 kB of archives. After this operation, 285 kB of additional disk space will be used. Do you want to continue? [Y/n] Y (Reading database ... 215368 files and directories currently installed.) Preparing to unpack .../libpng12-0_1.2.54-1ubuntu1.1_amd64.deb ... Unpacking libpng12-0:amd64 (1.2.54-1ubuntu1.1) ... dpkg: error processing archive /var/cache/apt/archives/libpng12-0_1.2.54-1ubuntu1.1_amd64.deb (--unpack): unable to install new version of '/lib/x86_64-linux-gnu/libpng12.so.0': No such file or directory No apport report written because the error message indicates an issue on the local system Errors were encountered while processing: /var/cache/apt/archives/libpng12-0_1.2.54-1ubuntu1.1_amd64.deb E: Sub-process /usr/bin/dpkg returned an error code (1)尝试解决：sudo dpkg -i --force-overwrite /var/cache/apt/archives/libpng12-0_1.2.54-1ubuntu1.1_amd64.deb 报错： (Reading database ... 215368 files and directories currently installed.) Preparing to unpack .../libpng12-0_1.2.54-1ubuntu1.1_amd64.deb ... Unpacking libpng12-0:amd64 (1.2.54-1ubuntu1.1) ... dpkg: error processing archive /var/cache/apt/archives/libpng12-0_1.2.54-1ubuntu1.1_amd64.deb (--install): unable to install new version of '/lib/x86_64-linux-gnu/libpng12.so.0': No such file or directory Processing triggers for libc-bin (2.29-0ubuntu2) ... Errors were encountered while processing: /var/cache/apt/archives/libpng12-0_1.2.54-1ubuntu1.1_amd64.deb接着运行：sudo apt-get -f install 报错： Reading package lists... Done Building dependency tree Reading state information... Done Correcting dependencies... Done The following additional packages will be installed: libpng12-0 The following NEW packages will be installed: libpng12-0 0 upgraded, 1 newly installed, 0 to remove and 40 not upgraded. 3 not fully installed or removed. Need to get 0 B/116 kB of archives. After this operation, 285 kB of additional disk space will be used. Do you want to continue? [Y/n] Y (Reading database ... 215368 files and directories currently installed.) Preparing to unpack .../libpng12-0_1.2.54-1ubuntu1.1_amd64.deb ... Unpacking libpng12-0:amd64 (1.2.54-1ubuntu1.1) ... dpkg: error processing archive /var/cache/apt/archives/libpng12-0_1.2.54-1ubuntu1.1_amd64.deb (--unpack): unable to install new version of '/lib/x86_64-linux-gnu/libpng12.so.0': No such file or directory No apport report written because the error message indicates an issue on the local system Errors were encountered while processing: /var/cache/apt/archives/libpng12-0_1.2.54-1ubuntu1.1_amd64.deb E: Sub-process /usr/bin/dpkg returned an error code (1) 添加适用于ubuntu版本的PPAsudo add-apt-repository ppa:linuxuprising/libpng12sudo apt updatesudo apt install libpng12-0然后openslide-tools顺利安装 安装python-openslide指令sudo apt-get install python-openslide 报错： root@node5-SYS-4029GP-TRT:~# sudo apt-get install python-openslide Reading package lists... Done Building dependency tree Reading state information... Done Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: python-openslide : Depends: python (= 2.7~) but it is not going to be installed Depends: python-pil but it is not going to be installed Depends: python:any (>= 2.7.5-5~) Recommends: python-openslide-examples but it is not going to be installed E: Unable to correct problems, you have held broken packages.换成python3-openslide：sudo apt-get install python3-openslide root@node5-SYS-4029GP-TRT:~# sudo apt-get install python3-openslide Reading package lists... Done Building dependency tree Reading state information... Done Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: python3-openslide : Depends: python3 (= 6) but it is not going to be installed libreadline6 : Depends: libtinfo5 (>= 6) but it is not going to be installed libreadline6-dev : Depends: libtinfo-dev but it is not going to be installed libsqlite3-dev : Depends: libsqlite3-0 (= 3.11.0-1ubuntu1.4) but 3.27.2-2ubuntu0.2 is to be installed libssl-dev : Depends: zlib1g-dev but it is not going to be installed sqlite3 : Depends: libsqlite3-0 (= 3.11.0-1ubuntu1.4) but 3.27.2-2ubuntu0.2 is to be installed E: Unable to correct problems, you have held broken packages. 手动配置依赖库例如：sudo apt-get install libbz2-1.0=1.0.6-8ubuntu0.2 然后提示了一个指令，好像是说autoremove什么的，执行了之后，集群就崩了。。。。。。 成功安装的方法集群重装系统后，按照github的教程2重新安装，直接安装成功，后来发现必须先安装openslide-tools，才能安装python3-openslide（python2就安装python-openslide）安装步骤： sudo apt-get install openslide-toolssudo apt-get install python3-openslide 或者 sudo apt-get install python-openslide（python2） 此时已经可以了cyq@NODE5:~$ python Python 3.6.6 |Anaconda, Inc.| (default, Jun 28 2018, 17:14:51) [GCC 7.2.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import openslide >>>如果是还要在conda虚拟环境下使用openslide，则继续进行下一步 3. pip install --no-deps openslide-python (keras) cyq@NODE5:~$ pip install --no-deps openslide-python Looking in indexes: http://pypi.tuna.tsinghua.edu.cn/simple/ Processing ./.cache/pip/wheels/a7/d4/0e/a41612c39c92873e6d5ae12cb8be3157b200003defea699dce/openslide_python-1.1.1-cp36-cp36m-linux_x86_64.whl Installing collected packages: openslide-python Successfully installed openslide-python-1.1.1 (keras) cyq@NODE5:~$ (keras) cyq@NODE5:~$ python Python 3.6.10 | packaged by conda-forge | (default, Apr 6 2020, 14:52:36) [GCC 7.3.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import openslide >>>完成～～ sudo apt-get update 各种问题！（ubuntu 16.04） ↩︎ python接口的openslide的安装教程 ↩︎ |
选择python接口下载，我选择的最新版本1.1.1
上传到集群，解压：tar -xzvf openslide-python-1.1.1.tar.gz 进入文件夹：cd openslide-python-1.1.1/ 安装：python setup.py install --single-version-externally-managed --record /dev/null 出现错误：【本文地址】
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