嘗試使用 rpy2 從 python 庫 rJava 時出錯

Question

嘗試使用rpy2 rJava時遇到問題。 我已經搜索並閱讀了許多問題，但沒有一個能解決我的問題。

我的rJava環境中的 rJava 安裝正常。

(base) pri@pri:~$ R

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

> library(data.table)
data.table 1.12.8 using 4 threads (see ?getDTthreads).  Latest news: r-datatable.com
> library(rJava)
> 

但是，當我嘗試使用rpy2從 Python 加載它時，出現錯誤：

(base) pri@pri:~$ python3
Python 3.7.7 (default, Mar 26 2020, 15:48:22) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import rpy2.robjects as robjects
>>> robjects.r('''library(data.table); library(rJava)''')
R[write to console]: data.table 1.12.8 using 4 threads (see ?getDTthreads).  Latest news: r-datatable.com

R[write to console]: Error: package or namespace load failed for ‘rJava’:
 .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/home/pri/R/x86_64-pc-linux-gnu-library/3.6/rJava/libs/rJava.so':
  libjvm.so: cannot open shared object file: No such file or directory

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/pri/anaconda3/lib/python3.7/site-packages/rpy2/robjects/__init__.py", line 416, in __call__
    res = self.eval(p)
  File "/home/pri/anaconda3/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 198, in __call__
    .__call__(*args, **kwargs))
  File "/home/pri/anaconda3/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 125, in __call__
    res = super(Function, self).__call__(*new_args, **new_kwargs)
  File "/home/pri/anaconda3/lib/python3.7/site-packages/rpy2/rinterface_lib/conversion.py", line 44, in _
    cdata = function(*args, **kwargs)
  File "/home/pri/anaconda3/lib/python3.7/site-packages/rpy2/rinterface.py", line 623, in __call__
    raise embedded.RRuntimeError(_rinterface._geterrmessage())
rpy2.rinterface_lib.embedded.RRuntimeError: Error: package or namespace load failed for ‘rJava’:
 .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/home/pri/R/x86_64-pc-linux-gnu-library/3.6/rJava/libs/rJava.so':
  libjvm.so: cannot open shared object file: No such file or directory

我已經檢查過二進制文件是否在正確的位置

(base) pri@pri:~$ ls /usr/lib/jvm/default-java/lib/server/
classes.jsa  libjsig.so  libjvm.so  Xusage.txt

並根據 linux 設置正確配置：

(base) pri@pri:~$ cat /usr/lib/R/etc/ldpaths | grep R_JAVA_LD_LIBRARY_PATH
: ${R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/server}
if test -n "${R_JAVA_LD_LIBRARY_PATH}"; then
  R_LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${R_JAVA_LD_LIBRARY_PATH}"

出於好奇，我還嘗試將 append 這個到 R 的.libPaths() ，但沒有成功：

JDBC_exe = "/usr/lib/jvm/default-java/lib/server/"
robjects.r('''.libPaths(c('{}', .libPaths()))'''\
            .format(JDBC_exe))

關於我在這里缺少什么以及如何解決這個問題的任何指針。

Answer 1

當通過以下命令確保環境變量LD_LIBRARY_PATH的值與 output 兼容時，與動態鏈接相關的大多數問題都應該解決：

python -m rpy2.situation LD_LIBRARY_PATH