rpy2 在脚本结束时产生无用的警告

Question

我是第一次使用py2r。一切正常，除了在我的脚本末尾，我在 stderr 上看到以下输出：

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :
R[write to console]: 
 
R[write to console]:  libraries ‘/usr/local/lib/R/site-library’, ‘/usr/lib/R/site-library’ contain no packages

这是一个 MRE：

import pandas as pd
import rpy2.robjects as ro
from rpy2.robjects.packages import importr
import rpy2.robjects.numpy2ri
rpy2.robjects.numpy2ri.activate()

df_counts = pd.DataFrame([[15, 25, 40, 23, 17, 40,],
                          [11, 22, 33, 22, 11, 33,],
                          [26, 36, 62, 48, 15, 62,]],
                         index=["A", "B", "C"],
                         columns=["ca_w", "ca_wo", "ca_n", "co_w", "co_wo", "co_n"])

r_exact2x2 = importr("exact2x2")
def get_sig_stats_from_r(cluster):
    ca_w = cluster["ca_w"]
    ca_wo = cluster["ca_wo"]
    ca_n = cluster["ca_n"]
    co_w = cluster["co_w"]
    co_wo = cluster["co_wo"]
    co_n = cluster["co_n"]

    uncond_exact = r_exact2x2.uncondExact2x2(ca_w, ca_n, co_w, co_n)
    fisher_table = ro.r.matrix(ro.vectors.IntVector([ca_w, co_w, ca_wo, co_wo]), nrow=2)
    fisher_exact = r_exact2x2.fisher_exact(fisher_table)
    uncond_p = uncond_exact.rx2("p.value")[0]
    fisher_p = fisher_exact.rx2("p.value")[0]
    fisher_OR = fisher_exact.rx2("estimate")[0]
    fisher_CI = fisher_exact.rx2("conf.int")
    fisher_CI = list(fisher_CI)

    return [uncond_p, fisher_p, fisher_OR, fisher_CI]

df_sig = df_counts.apply(get_sig_stats_from_r, axis=1, result_type="expand")
print(df_sig)
df_sig.to_csv("foo.csv")

并且输出：

          0         1         2                 3
A  0.086901  0.116535  0.448134  [0.1755, 1.1045]
B  0.009209  0.013221  0.255747  [0.0891, 0.7303]
C  0.000051  0.000123  0.228655  [0.1015, 0.4998]
R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :
R[write to console]: 
 
R[write to console]:  libraries ‘/usr/local/lib/R/site-library’, ‘/usr/lib/R/site-library’ contain no packages

这似乎不是正确的警告，因为 warnings.simplefilter("ignore") 不会停止消息。这在虚拟环境和系统（用户）python3.

中都会发生

这是什么意思，我该如何阻止它？这是否表示可能会在其他人的系统上导致实际错误？

提前致谢。

Answer 1

可以说，警告的用处在于旁观者。

这里发生的事情是 R 发出了一个警告，据我所知，该警告与令人惊讶的空目录有关。在不了解更多的情况下很难判断是否有什么值得担心的，但我建议检查一下 R 在该系统上的安装方式。

否则可以通过自定义回调来使 R 的此类消息静音（请参阅文档 - https://rpy2.github.io/doc/v3.3.x/html/callbacks.html#write-console) or through the logger used by the default callback (see the code - https://github.com/rpy2/rpy2/blob/master/rpy2/rinterface_lib/callbacks.py#L119）。

rpy2 在脚本结束时产生无用的警告

rpy2 produces useless warning on script end

python

r

warnings

rpy2