我正在尝试在我正在使用的 HPC 上安装 SynapseR，以便我可以从那里运行我的脚本。
install.packages("synapser", repos=c("http://staging-ran.synapse.org"))
给我错误：
Installing package into ‘/kyukon/home/gent/456/vsc45640/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'http://staging-ran.synapse.org/src/contrib/synapser_1.0.57.tar.gz'
Content type 'application/x-tar' length 154291 bytes (150 KB)
==================================================
downloaded 150 KB
* installing *source* package ‘synapser’ ...
** using staged installation
[1] "*** Using Python Configuration:"
python: /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/bin/python
libpython: /usr/lib64/libpython3.6m.so
pythonhome: /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate:/kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate
version: 3.6.8 (default, Jun 14 2022, 12:54:58) [GCC 8.5.0 20210514 (Red Hat 8.5.0-10)]
numpy: /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages/numpy
numpy_version: 1.19.5
python versions found:
/kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/bin/python
/kyukon/home/apps/RHEL8/zen3-ampere-ib/software/Python/3.9.6-GCCcore-11.2.0/bin/python3
/kyukon/home/apps/RHEL8/zen3-ampere-ib/software/Python/3.9.6-GCCcore-11.2.0/bin/python
/usr/bin/python3
/usr/bin/python
Using virtual environment '/kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate' ...
+ '/kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/bin/python' -m pip install --upgrade --no-user 'requests' 'pandas' 'pysftp' 'jinja2' 'markupsafe'
Requirement already satisfied: requests in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (2.27.1)
Requirement already satisfied: pandas in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (1.1.5)
Requirement already satisfied: pysftp in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (0.2.9)
Requirement already satisfied: jinja2 in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (3.0.3)
Requirement already satisfied: markupsafe in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (2.0.1)
Requirement already satisfied: charset-normalizer~=2.0.0 in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (from requests) (2.0.12)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (from requests) (1.26.15)
Requirement already satisfied: certifi>=2017.4.17 in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (from requests) (2023.5.7)
Requirement already satisfied: idna<4,>=2.5 in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (from requests) (3.4)
Requirement already satisfied: numpy>=1.15.4 in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (from pandas) (1.19.5)
Requirement already satisfied: python-dateutil>=2.7.3 in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (from pandas) (2.8.2)
Requirement already satisfied: pytz>=2017.2 in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (from pandas) (2023.3)
Requirement already satisfied: paramiko>=1.17 in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (from pysftp) (3.1.0)
Requirement already satisfied: bcrypt>=3.2 in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (from paramiko>=1.17->pysftp) (4.0.1)
Requirement already satisfied: pynacl>=1.5 in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (from paramiko>=1.17->pysftp) (1.5.0)
Requirement already satisfied: cryptography>=3.3 in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (from paramiko>=1.17->pysftp) (40.0.2)
Requirement already satisfied: six>=1.5 in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (from python-dateutil>=2.7.3->pandas) (1.16.0)
Requirement already satisfied: cffi>=1.12 in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (from cryptography>=3.3->paramiko>=1.17->pysftp) (1.15.1)
Requirement already satisfied: pycparser in /kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/lib/python3.6/site-packages (from cffi>=1.12->cryptography>=3.3->paramiko>=1.17->pysftp) (2.21)
Using virtual environment '/kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate' ...
+ '/kyukon/home/gent/456/vsc45640/.virtualenvs/r-reticulate/bin/python' -m pip install --upgrade --no-user 'synapseclient==2.7.0'
ERROR: Could not find a version that satisfies the requirement synapseclient==2.7.0 (from versions: 0.1.2, 0.1.4, 0.2.0, 0.2.1, 0.3.0, 0.4.0, 0.4.1, 0.5.0, 0.5.1, 0.5.2, 1.0.1, 1.0.3, 1.1, 1.2, 1.3, 1.4, 1.5, 1.5.1, 1.6.1, 1.6.2, 1.7.1, 1.7.2, 1.7.3, 1.7.5, 1.8.0, 1.8.1, 1.8.2, 1.9.0, 1.9.1, 1.9.2, 1.9.3, 1.9.4, 2.0.0, 2.1.0, 2.1.1, 2.2.0, 2.2.2, 2.3.0, 2.3.1, 2.4.0, 2.5.0, 2.5.1)
ERROR: No matching distribution found for synapseclient==2.7.0
Error: Error installing package(s): "'synapseclient==2.7.0'"
Execution halted
ERROR: configuration failed for package ‘synapser’
* removing ‘/kyukon/home/gent/456/vsc45640/R/x86_64-pc-linux-gnu-library/4.2/synapser’
Warning in install.packages :
installation of package ‘synapser’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmpm6z0Np/downloaded_packages’
有人可以帮助我吗？
我已经尝试自行安装 synapseclient，但没有成功
有一段时间遇到同样的问题，尝试安装 synapser。这是我运行的解决方法。它比安装一个简单的 R 库需要更抽象一些，但它可以在我的机器上运行。
在他们的 github 上，他们有一个 dockerfile，可以帮助您完成大部分工作。您需要将此文件复制到本地目录中，然后构建图像
docker build -t synapser .
这里的synapser是docker容器的名称。在运行之前，您需要创建一个位置来存储数据，我称之为“./data”，然后您可以使用此命令运行交互式 R 终端
docker run -v ./data:/data -it synapser
并检查以确保已安装 synapser
library(synapser)
输出：
“使用条款通知： 使用 Synapse 时，...”
将数据保存在容器内部的 /data 中，容器关闭后它将保留。
唷，“简单”安装需要做很多工作。