rpy2在脚本结束时产生无用的警告

Question

我是第一次使用py2r。除了在脚本结束时，我在stderr上看到以下输出之外，一切都很好：

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")

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

它似乎不是一个适当的警告作为警告。simplefilter("忽略"(不会停止消息。这在虚拟环境和系统(用户(python3中都会发生。

这意味着什么？我该如何阻止它？这是否表明可能导致他人系统出现实际错误？

提前谢谢。

Answer 1

可以说，警告的有用性在于旁观者。

这里发生的事情是，R发出了一个警告，据我所知，这与令人惊讶的空目录有关。如果不了解更多信息，很难说是否有什么值得担心的，但我建议检查R是如何安装在该系统上的。

否则，可以通过自定义回调来静音R的此类消息(请参阅文档-https://rpy2.github.io/doc/v3.3.x/html/callbacks.html#write-控制台(或通过默认回调使用的记录器(请参阅代码-https://github.com/rpy2/rpy2/blob/master/rpy2/rinterface_lib/callbacks.py#L119)。