在特定数据集上调用“write.table"时崩溃 R [英] Crashing R when calling `write.table` on particular data set
问题描述
以下内容始终使我的 R 会话崩溃.
在两台机器上测试，Ubuntu 和 Mac OS X，两者的结果相似.
The following consistently crashes my R session.
Tested on two machines, Ubuntu and Mac OS X with similar results on both.
简要说明:
在具有所有 NA 的因子列的 data.frame 上调用 write.table.
原始数据集相当大，我设法隔离了有问题的列，然后创建了一个类似的向量，在下面命名为 PROBLEM_DATA，这会导致同样的崩溃.
The original data set is rather large, and I've managed to isolate the offending column and then create a similar vector, named PROBLEM_DATA below, which causes the same crash.
有趣的是，有时 R 会直接崩溃，有时它只是抛出以下错误:
Interestingly, sometimes R crashes outright, othertimes it simply throws the following error:
Error in write.table(x, file, nrow(x), p, rnames, sep, eol, na, dec, as.integer(quote), :
'getCharCE' must be called on a CHARSXP
关于崩溃原因的任何想法还是应该将其作为错误提交?
违规数据和调用:
Any thoughts as to the cause of the crash or should it be submitted as a bug?
Offending data and call:
PROBLEM_DATA <- structure(114:116, .Label = c("String1", "String2", "String3", "String4", "String5", "String6",
"String7", "String8", "String9", "String10", "String11", "String12", "String13", "String14", "String15"), class = "factor")
# This will cause a crash
write.table(PROBLEM_DATA, file=path.expand("~/test.csv"))
# This will also crash
write.table(PROBLEM_DATA, file=path.expand("~/test.csv"), fileEncoding="UTF-8")
每台机器的会话信息
UBUNTU
R version 2.15.3 (2013-03-01)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C
[5] LC_MONETARY=C LC_MESSAGES=C LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] gdata_2.12.0 ggplot2_0.9.3 stringr_0.6.1 RMySQL_0.9-3 DBI_0.2-5
[6] data.table_1.8.8
loaded via a namespace (and not attached):
[1] MASS_7.3-23 RColorBrewer_1.0-5 colorspace_1.2-0 dichromat_1.2-4
[5] digest_0.5.2 grid_2.15.3 gtable_0.1.1 gtools_2.7.0
[9] labeling_0.1 munsell_0.4 plyr_1.7.1 proto_0.3-9.2
[13] reshape2_1.2.1 scales_0.2.3 tools_2.15.3
Mac OS X
R version 2.15.3 (2013-03-01)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
推荐答案
这是一个很好的可重现错误，应报告给 R-devel 或使用 bug.report().FWIW 上
This is a nice reproducible bug and should be reported to R-devel or using bug.report(). FWIW on
> sessionInfo()
R version 3.0.0 Patched (2013-04-03 r62485)
Platform: x86_64-unknown-linux-gnu (64-bit)
如果在 Linux 上我用 CFLAGS="-g -O0" 配置 R，我可以
If on Linux I configure R with CFLAGS="-g -O0" I can
R -d gdb
(gdb) break Rf_error
(gdb) run
然后在上面粘贴你的行并结束
then paste your lines above and end up at
> write.table(PROBLEM_DATA, file=path.expand("~/test.csv"))
Breakpoint 1, Rf_error (format=0x7ffff7a8f0f0 "'%s' must be called on a CHARSXP") at /home/mtmorgan/src/R-3-0-branch/src/main/errors.c:753
753 RCNTXT *c = R_GlobalContext;
(gdb) up 3
#3 0x00007ffff1b9bfb3 in EncodeElement2 (x=0x31ccf50, indx=113, quote=TRUE, qmethod=TRUE, buff=0x7fffffffbdc0, cdec=46 '.')
at /home/mtmorgan/src/R-3-0-branch/src/library/utils/src/io.c:938
938 p0 = translateChar(STRING_ELT(x, indx));
(gdb) call Rf_PrintValue(x)
[1] "String1" "String2" "String3" "String4" "String5" "String6"
[7] "String7" "String8" "String9" "String10" "String11" "String12"
[13] "String13" "String14" "String15"
(gdb) p indx
$1 = 113
这表明 R 试图打印出因子名称的第 114 个元素 - 显然事情出错了，因为该因子具有超出其级别长度的整数值.
which shows R trying to print out the 114th element of the factor names -- clearly things have gone wrong because the factor has integer values beyond the length of its levels.
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