Question

我正在尝试使用system中的R函数来运行程序，我希望在某些情况下会产生错误消息。为此，我想写一个tryCatch函数。

system(command, intern = TRUE)只返回我正在运行的程序回显的实际值，它不会返回我的错误。

在R中，如何获取系统产生的错误消息？

我的代码：

test <- tryCatch({
cmd <- paste0("../Scripts/Plink2/plink --file ../InputData/",prefix," --bmerge ",
"../InputData/fs --missing --out ../InputData/",prefix)
print(cmd)
system(cmd)
} , error = function(e) {
  # error handler picks up where error was generated
  print("EZEL")
  print(paste("MY_ERROR:  ",e))
}, finally = {
  print("something")
})
[1] "../Scripts/Plink2/plink --file ../InputData/GS80Kdata --bmerge ../InputData/fs --missing --out ../InputData/GS80Kdata"
PLINK v1.90b3.37 64-bit (16 May 2016)      https://www.cog-genomics.org/plink2
#....
#skipping some lines here to reduce size
#....
Of these, 1414410 are new, while 2462 are present in the base dataset.
Error: 1 variant with 3+ alleles present.
* If you believe this is due to strand inconsistency, try --flip with
# Skipping some more lines here    
[1] "something"

但是，当使用intern=TRUE并将系统函数分配给变量时，不会捕获向量中的错误并仍然将其打印在R控制台中。

编辑：这里是矢量的输出（使用gsub来减少荒谬的大小）

> gsub(pattern="\b\\d.*", replacement = "", x = tst)
 [1] "PLINK v1.90b3.37 64-bit (16 May 2016)      https://www.cog-genomics.org/plink2"
 [2] "(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3"
 [3] "Logging to ../InputData/GS80Kdata.log."
 [4] "Options in effect:"
 [5] "  --bmerge ../InputData/fs"
 [6] "  --file ../InputData/GS80Kdata"
 [7] "  --missing"
 [8] "  --out ../InputData/GS80Kdata"
 [9] ""
[10] "64381 MB RAM detected; reserving 32190 MB for main workspace."
[11] "Scanning .ped file... 0%\b"
[12] "2%\b\b"
[13] "%\b\b"
[14] "\b\b"
[15] "\b"
[16] ""
[17] "58%\b\b"
[18] "7%\b\b"
[19] "%\b\b"
[20] "\b\b"
[21] "\b"
[22] "Performing single-pass .bed write (42884 variants, 14978 people)."
[23] "0%\b"
[24] "../InputData/GS80Kdata-temporary.bim + ../InputData/GS80Kdata-temporary.fam"
[25] "written."
[26] "14978 people loaded from ../InputData/GS80Kdata-temporary.fam."
[27] "144 people to be merged from ../InputData/fs.fam."
[28] "Of these, 140 are new, while 4 are present in the base dataset."
[29] "42884 markers loaded from ../InputData/GS80Kdata-temporary.bim."
[30] "1416872 markers to be merged from ../InputData/fs.bim."
[31] "Of these, 1414410 are new, while 2462 are present in the base dataset."
attr(,"status")
[1] 3
>

如何在R中打印系统调用的错误

0 个答案: