eip*_*i10 11 r segmentation-fault reshape2
当我尝试使用dcast(从reshape2包中)重塑特定数据帧时,RStudio崩溃了.我发现崩溃实际上发生在R本身,所以我在R.app中运行了我的强制转换代码并得到了错误类型,它给这个站点起了名字:Error: segfault from C stack overflow.在Google和SO的帮助下,我了解到这是一个内存访问错误.
好的,我走得那么远,但我不知道从哪里开始.我无法提供真正可重现的示例,因为我的数据框大约是558,000行,并且小玩具示例中不会出现此问题.例如,即使我拿了一个50,000行的数据子集,也dcast可以正常工作.是否会出现导致问题的特定数据行？如果是这样,任何人都可以建议寻找哪些功能可能导致我得到的错误类型？
这是我正在构建的数据框的子集(对于某些变量使用伪值),然后是我正在使用的转换函数.我还在dput下面的函数中包含了这一小段数据,以防它玩起来有所帮助.实际数据集具有约700个值prog,15个值prog1和5个值fa.type.
id term yr nslds acad.lev prog prog1 fa.type amount
1 1 Fall 2009 2010 Graduate Graduate loan 1 Other Loans Loan 5000
2 1 Spring 2010 2010 Graduate Graduate loan 1 Other Loans Loan 5000
3 2 Fall 2009 2010 Graduate Graduate loan 2 Stafford Loan Loan 8781
4 2 Spring 2010 2010 Graduate Graduate loan 2 Stafford Loan Loan 8781
5 3 Fall 2007 2008 Graduate Graduate loan 3 Stafford Loan Loan 4250
6 3 Fall 2007 2008 Graduate Graduate grant 1 University Grant Grant 1707
fa.wide = dcast(id + term + yr + nslds + acad.lev ~ prog1 + fa.type , data=fa, value.var="amount", fun.aggregate=sum)
fa = structure(list(id = c(1, 1, 2, 2, 3, 3), term = structure(c(7L,
8L, 7L, 8L, 1L, 1L), .Label = c("Fall 2007", "Spring 2008", "Summer 2008",
"Fall 2008", "Spring 2009", "Summer 2009", "Fall 2009", "Spring 2010",
"Summer 2010", "Fall 2010", "Spring 2011", "Summer 2011", "Fall 2011",
"Spring 2012", "Summer 2012", "Fall 2012", "Spring 2013"), class = c("ordered",
"factor")), yr = c(2010L, 2010L, 2010L, 2010L, 2008L, 2008L),
nslds = structure(c(7L, 7L, 7L, 7L, 7L, 7L), .Label = c("1st Year, Never Attended",
"1st Year, Previously Attended", "2nd Year", "3rd Year",
"4th Year", "5th Year+", "Graduate"), class = c("ordered",
"factor")), acad.lev = structure(c(6L, 6L, 6L, 6L, 6L, 6L
), .Label = c("Freshman", "Sophomore", "Junior", "Senior",
"PB Undergrad", "Graduate"), class = c("ordered", "factor"
)), prog = c("loan 1", "loan 1", "loan 2", "loan 2", "loan 3",
"grant 1"), prog1 = c("Other Loans", "Other Loans", "Stafford Loan",
"Stafford Loan", "Stafford Loan", "University Grant"), fa.type = structure(c(3L,
3L, 3L, 3L, 3L, 2L), .Label = c("Athletic", "Grant", "Loan",
"Scholarship", "Waiver", "Work/Study"), class = "factor"),
amount = c(5000, 5000, 8781, 8781, 4250, 1707)), .Names = c("id",
"term", "yr", "nslds", "acad.lev", "prog", "prog1", "fa.type",
"amount"), row.names = c(NA, 6L), class = "data.frame")
这不是一个答案,而是一个简单(非感性)可重复的例子,不适合评论.您可以使用此简单示例(在我的MacBookPro上)重新创建此错误.
require(reshape2)
n = 1448
df <- data.frame( Student = rep( 1:n , each = 2 ) , Grade = sample( 100 , n*2 , repl = TRUE ) )
df2 <- dcast( df , Student ~ Student , value.var = "Grade" , sum )
Error: segfault from C stack overflow
错误发生在边界处n = 1448,即在n=1447下方时不会发生.看来,错误是来自split_indices于split-numeric.c从包plyr.这可能与该分组级别的数量分配给(无符号？)整数值的事实做,如果组数越过32767它会导致一个内存访问错误,但TBH我救命稻草,现在抓着.
我sessionInfo()万一有人无法重新创建此错误是:
R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] reshape2_1.2.2
loaded via a namespace (and not attached):
[1] plyr_1.8 stringr_0.6.2
有趣的是,如果我df2 <-在收到第一个错误后再次运行命令,R会完全崩溃并且我会收到一些操作系统生成的错误报告.我在此处包含崩溃日志的相关部分:
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_PROTECTION_FAILURE at 0x00007fff5f3ff120
VM Regions Near 0x7fff5f3ff120:
JS JIT generated code 00004d431a401000-00004d431a402000 [ 4K] ---/rwx SM=NUL
--> STACK GUARD 00007fff5bc00000-00007fff5f400000 [ 56.0M] ---/rwx SM=NUL stack guard for thread 0
Stack 00007fff5f400000-00007fff5fc00000 [ 8192K] rw-/rwx SM=COW thread 0
Application Specific Information:
objc[57147]: garbage collection is OFF
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_c.dylib 0x00007fff897c4632 small_free_scan_madvise_free + 41
1 libsystem_c.dylib 0x00007fff897c5f06 szone_free_definite_size + 4186
2 libsystem_c.dylib 0x00007fff897fe789 free + 194
3 libR.dylib 0x0000000100222dbf R_gc_internal + 7327 (memory.c:952)
4 libR.dylib 0x0000000100224919 Rf_allocVector + 841 (memory.c:2356)
5 plyr.so 0x000000010144bd2c split_indices + 204 (split-numeric.c:23)
6 libR.dylib 0x00000001001b4cc7 do_dotcall + 16311 (dotcode.c:593)
7 libR.dylib 0x00000001001e4448 Rf_eval + 1672 (eval.c:494)
8 libR.dylib 0x00000001001e5edd do_begin + 141 (eval.c:1415)
9 libR.dylib 0x00000001001e429c Rf_eval + 1244 (eval.c:468)
10 libR.dylib 0x00000001001e93b1 Rf_applyClosure + 849 (eval.c:861)
11 libR.dylib 0x00000001001e41b2 Rf_eval + 1010 (eval.c:512)
12 libR.dylib 0x00000001001e74e5 do_set + 709 (eval.c:1717)
13 libR.dylib 0x00000001001e429c Rf_eval + 1244 (eval.c:468)
14 libR.dylib 0x00000001001e5edd do_begin + 141 (eval.c:1415)
15 libR.dylib 0x00000001001e429c Rf_eval + 1244 (eval.c:468)
16 libR.dylib 0x00000001001e93b1 Rf_applyClosure + 849 (eval.c:861)
17 libR.dylib 0x00000001001e41b2 Rf_eval + 1010 (eval.c:512)
18 libR.dylib 0x00000001001e74e5 do_set + 709 (eval.c:1717)
19 libR.dylib 0x00000001001e429c Rf_eval + 1244 (eval.c:468)
20 libR.dylib 0x00000001001e5edd do_begin + 141 (eval.c:1415)
21 libR.dylib 0x00000001001e429c Rf_eval + 1244 (eval.c:468)
22 libR.dylib 0x00000001001e429c Rf_eval + 1244 (eval.c:468)
23 libR.dylib 0x00000001001e5edd do_begin + 141 (eval.c:1415)
24 libR.dylib 0x00000001001e429c Rf_eval + 1244 (eval.c:468)
25 libR.dylib 0x00000001001e93b1 Rf_applyClosure + 849 (eval.c:861)
26 libR.dylib 0x00000001001e41b2 Rf_eval + 1010 (eval.c:512)
27 libR.dylib 0x00000001001e74e5 do_set + 709 (eval.c:1717)
28 libR.dylib 0x00000001001e429c Rf_eval + 1244 (eval.c:468)
29 libR.dylib 0x00000001001e5edd do_begin + 141 (eval.c:1415)
30 libR.dylib 0x00000001001e429c Rf_eval + 1244 (eval.c:468)
31 libR.dylib 0x00000001001e93b1 Rf_applyClosure + 849 (eval.c:861)
32 libR.dylib 0x00000001001e41b2 Rf_eval + 1010 (eval.c:512)
33 libR.dylib 0x00000001001e74e5 do_set + 709 (eval.c:1717)
34 libR.dylib 0x00000001001e429c Rf_eval + 1244 (eval.c:468)
35 libR.dylib 0x000000010021c761 R_ReplDLLdo1 + 481 (main.c:362)
36 org.R-project.R 0x0000000100022c24 run_REngineRmainloop + 196
37 org.R-project.R 0x00000001000159b7 -[REngine runREPL] + 119
38 org.R-project.R 0x0000000100001f24 main + 852
39 org.R-project.R 0x0000000100001914 start + 52