RStudio crashes after running code then editing script

WillH · March 26, 2019, 5:59pm

Crash Information:

When I run ~500 lines and then try to edit the content of the script (without running it) R seems to crash.

I have tried:

deleting .Rdata
creating a fresh .Rproj.user by moving the existing one to another directory and opening RStudio
Uninstalling then reintalling RStudio

Description of crash -
R Session Aborted: R encountered a fatal error. The session was terminated

Steps to reproduce -

As described above

System Information:

RStudio Edition: Desktop
RStudio Version: 1.1.463
OS Version: macOS Mojave 10.14.4
R Version: 3.5.2
Your sessionInfo():

Crash Report:

Process:               rsession [1696]
Path:                  /Applications/RStudio.app/Contents/MacOS/rsession
Identifier:            rsession
Version:               ???
Code Type:             X86-64 (Native)
Parent Process:        RStudio [1686]
Responsible:           rsession [1696]
User ID:               501

Date/Time:             2019-03-07 14:30:44.291 +0000
OS Version:            Mac OS X 10.14.3 (18D109)
Report Version:        12
Anonymous UUID:        BE010E8E-8824-9504-2B8F-E118D9F1C2A8

Sleep/Wake UUID:       B9481933-7D26-4EB1-A30E-D4280A6B948A

Time Awake Since Boot: 12000 seconds
Time Since Wake:       350 seconds

System Integrity Protection: enabled

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x000000000002610e
Exception Note:        EXC_CORPSE_NOTIFY

VM Regions Near 0x2610e:
--> 
    __TEXT                 0000000100000000-0000000100be5000 [ 11.9M] r-x/rwx SM=COW  /Applications/RStudio.app/Contents/MacOS/rsession

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   libjvm.dylib                  	0x0000000121cdbd1f resource_allocate_bytes(unsigned long, AllocFailStrategy::AllocFailEnum) + 27
1   libjvm.dylib                  	0x0000000121b4e48a JVM_GetStackAccessControlContext + 112
2   ???                           	0x0000000176fec9f4 0 + 6291376628
3   ???                           	0x0000000176fdd040 0 + 6291312704
4   ???                           	0x0000000176fdd040 0 + 6291312704
5   ???                           	0x0000000176fdd2bd 0 + 6291313341
6   ???                           	0x0000000176fdd2bd 0 + 6291313341
7   ???                           	0x0000000176fd57a7 0 + 6291281831
8   libjvm.dylib                  	0x0000000122a90bd2 JavaCalls::call_helper(JavaValue*, methodHandle*, JavaCallArguments*, Thread*) + 1710
9   libjvm.dylib                  	0x0000000122a9104a JavaCalls::call_special(JavaValue*, KlassHandle, Symbol*, Symbol*, JavaCallArguments*, Thread*) + 252
10  libjvm.dylib                  	0x0000000122a9113e JavaCalls::call_special(JavaValue*, Handle, KlassHandle, Symbol*, Symbol*, Handle, Handle, Thread*) + 118
11  libjvm.dylib                  	0x0000000122d106ab Threads::create_vm(JavaVMInitArgs*, bool*) + 1623
12  libjvm.dylib                  	0x0000000122ac70b3 JNI_CreateJavaVM + 118
13  rJava.so                      	0x00000001067c1764 RinitJVM + 1076 (init.c:144)
14  libR.dylib                    	0x000000010120c46d do_External + 301
15  libR.dylib                    	0x0000000101242ba8 bcEval + 19608 (eval.c:6781)
16  libR.dylib                    	0x000000010123d7db Rf_eval + 443
17  libR.dylib                    	0x000000010125014c R_execClosure + 3004
18  libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
19  libR.dylib                    	0x000000010123d7db Rf_eval + 443
20  libR.dylib                    	0x000000010125014c R_execClosure + 3004
21  libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
22  libR.dylib                    	0x000000010123d7db Rf_eval + 443
23  libR.dylib                    	0x000000010125014c R_execClosure + 3004
24  libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
25  libR.dylib                    	0x000000010123d7db Rf_eval + 443
26  libR.dylib                    	0x000000010124e513 forcePromise + 179 (eval.c:520)
27  libR.dylib                    	0x0000000101259106 getvar + 518 (eval.c:4983)
28  libR.dylib                    	0x0000000101240fcc bcEval + 12476 (eval.c:6513)
29  libR.dylib                    	0x000000010123d7db Rf_eval + 443
30  libR.dylib                    	0x000000010124e513 forcePromise + 179 (eval.c:520)
31  libR.dylib                    	0x0000000101259106 getvar + 518 (eval.c:4983)
32  libR.dylib                    	0x0000000101240fcc bcEval + 12476 (eval.c:6513)
33  libR.dylib                    	0x000000010123d7db Rf_eval + 443
34  libR.dylib                    	0x000000010124e513 forcePromise + 179 (eval.c:520)
35  libR.dylib                    	0x0000000101259106 getvar + 518 (eval.c:4983)
36  libR.dylib                    	0x0000000101240fcc bcEval + 12476 (eval.c:6513)
37  libR.dylib                    	0x000000010123d7db Rf_eval + 443
38  libR.dylib                    	0x000000010124e513 forcePromise + 179 (eval.c:520)
39  libR.dylib                    	0x0000000101259106 getvar + 518 (eval.c:4983)
40  libR.dylib                    	0x0000000101240fcc bcEval + 12476 (eval.c:6513)
41  libR.dylib                    	0x000000010123d7db Rf_eval + 443
42  libR.dylib                    	0x000000010125014c R_execClosure + 3004
43  libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
44  libR.dylib                    	0x000000010123d7db Rf_eval + 443
45  libR.dylib                    	0x000000010125014c R_execClosure + 3004
46  libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
47  libR.dylib                    	0x000000010123d7db Rf_eval + 443
48  libR.dylib                    	0x000000010125014c R_execClosure + 3004
49  libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
50  libR.dylib                    	0x000000010123d7db Rf_eval + 443
51  libR.dylib                    	0x000000010125014c R_execClosure + 3004
52  libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
53  libR.dylib                    	0x000000010123d7db Rf_eval + 443
54  libR.dylib                    	0x000000010125014c R_execClosure + 3004
55  libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
56  libR.dylib                    	0x000000010123d7db Rf_eval + 443
57  libR.dylib                    	0x000000010125014c R_execClosure + 3004
58  libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
59  libR.dylib                    	0x000000010123d7db Rf_eval + 443
60  libR.dylib                    	0x000000010124e513 forcePromise + 179 (eval.c:520)
61  libR.dylib                    	0x000000010123d862 Rf_eval + 578
62  libR.dylib                    	0x0000000101241eb6 bcEval + 16294 (eval.c:6697)
63  libR.dylib                    	0x000000010123d7db Rf_eval + 443
64  libR.dylib                    	0x000000010125014c R_execClosure + 3004
65  libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
66  libR.dylib                    	0x000000010123d7db Rf_eval + 443
67  libR.dylib                    	0x000000010125014c R_execClosure + 3004
68  libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
69  libR.dylib                    	0x000000010123d7db Rf_eval + 443
70  libR.dylib                    	0x000000010124e513 forcePromise + 179 (eval.c:520)
71  libR.dylib                    	0x0000000101259106 getvar + 518 (eval.c:4983)
72  libR.dylib                    	0x0000000101240fcc bcEval + 12476 (eval.c:6513)
73  libR.dylib                    	0x000000010123d7db Rf_eval + 443
74  libR.dylib                    	0x000000010124e513 forcePromise + 179 (eval.c:520)
75  libR.dylib                    	0x0000000101259106 getvar + 518 (eval.c:4983)
76  libR.dylib                    	0x0000000101240fcc bcEval + 12476 (eval.c:6513)
77  libR.dylib                    	0x000000010123d7db Rf_eval + 443
78  libR.dylib                    	0x000000010124e513 forcePromise + 179 (eval.c:520)
79  libR.dylib                    	0x0000000101259106 getvar + 518 (eval.c:4983)
80  libR.dylib                    	0x0000000101240fcc bcEval + 12476 (eval.c:6513)
81  libR.dylib                    	0x000000010123d7db Rf_eval + 443
82  libR.dylib                    	0x000000010124e513 forcePromise + 179 (eval.c:520)
83  libR.dylib                    	0x0000000101259106 getvar + 518 (eval.c:4983)
84  libR.dylib                    	0x0000000101240fcc bcEval + 12476 (eval.c:6513)
85  libR.dylib                    	0x000000010123d7db Rf_eval + 443
86  libR.dylib                    	0x000000010125014c R_execClosure + 3004
87  libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
88  libR.dylib                    	0x000000010123d7db Rf_eval + 443
89  libR.dylib                    	0x000000010125014c R_execClosure + 3004
90  libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
91  libR.dylib                    	0x000000010123d7db Rf_eval + 443
92  libR.dylib                    	0x000000010125014c R_execClosure + 3004
93  libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
94  libR.dylib                    	0x000000010123d7db Rf_eval + 443
95  libR.dylib                    	0x000000010125014c R_execClosure + 3004
96  libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
97  libR.dylib                    	0x000000010123d7db Rf_eval + 443
98  libR.dylib                    	0x000000010125014c R_execClosure + 3004
99  libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
100 libR.dylib                    	0x000000010123d7db Rf_eval + 443
101 libR.dylib                    	0x000000010124e513 forcePromise + 179 (eval.c:520)
102 libR.dylib                    	0x0000000101259106 getvar + 518 (eval.c:4983)
103 libR.dylib                    	0x0000000101240fcc bcEval + 12476 (eval.c:6513)
104 libR.dylib                    	0x000000010123d7db Rf_eval + 443
105 libR.dylib                    	0x000000010124e513 forcePromise + 179 (eval.c:520)
106 libR.dylib                    	0x0000000101259106 getvar + 518 (eval.c:4983)
107 libR.dylib                    	0x0000000101240fcc bcEval + 12476 (eval.c:6513)
108 libR.dylib                    	0x000000010123d7db Rf_eval + 443
109 libR.dylib                    	0x000000010125014c R_execClosure + 3004
110 libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
111 libR.dylib                    	0x000000010123d7db Rf_eval + 443
112 libR.dylib                    	0x000000010125014c R_execClosure + 3004
113 libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
114 libR.dylib                    	0x000000010123d7db Rf_eval + 443
115 libR.dylib                    	0x000000010124e513 forcePromise + 179 (eval.c:520)
116 libR.dylib                    	0x0000000101259106 getvar + 518 (eval.c:4983)
117 libR.dylib                    	0x0000000101240fcc bcEval + 12476 (eval.c:6513)
118 libR.dylib                    	0x000000010123d7db Rf_eval + 443
119 libR.dylib                    	0x000000010124e513 forcePromise + 179 (eval.c:520)
120 libR.dylib                    	0x0000000101259106 getvar + 518 (eval.c:4983)
121 libR.dylib                    	0x0000000101240fcc bcEval + 12476 (eval.c:6513)
122 libR.dylib                    	0x000000010123d7db Rf_eval + 443
123 libR.dylib                    	0x000000010124e513 forcePromise + 179 (eval.c:520)
124 libR.dylib                    	0x0000000101259106 getvar + 518 (eval.c:4983)
125 libR.dylib                    	0x0000000101240fcc bcEval + 12476 (eval.c:6513)
126 libR.dylib                    	0x000000010123d7db Rf_eval + 443
127 libR.dylib                    	0x000000010124e513 forcePromise + 179 (eval.c:520)
128 libR.dylib                    	0x0000000101259106 getvar + 518 (eval.c:4983)
129 libR.dylib                    	0x0000000101240fcc bcEval + 12476 (eval.c:6513)
130 libR.dylib                    	0x000000010123d7db Rf_eval + 443
131 libR.dylib                    	0x000000010125014c R_execClosure + 3004
132 libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
133 libR.dylib                    	0x000000010123d7db Rf_eval + 443
134 libR.dylib                    	0x000000010125014c R_execClosure + 3004
135 libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
136 libR.dylib                    	0x000000010123d7db Rf_eval + 443
137 libR.dylib                    	0x000000010125014c R_execClosure + 3004
138 libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
139 libR.dylib                    	0x000000010123d7db Rf_eval + 443
140 libR.dylib                    	0x000000010125014c R_execClosure + 3004
141 libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
142 libR.dylib                    	0x000000010123d7db Rf_eval + 443
143 libR.dylib                    	0x000000010125014c R_execClosure + 3004
144 libR.dylib                    	0x00000001012427f3 bcEval + 18659 (eval.c:6749)
145 libR.dylib                    	0x000000010123d7db Rf_eval + 443
146 libR.dylib                    	0x000000010125014c R_execClosure + 3004
147 libR.dylib                    	0x000000010123dd0c Rf_eval + 1772 (eval.c:747)
148 libR.dylib                    	0x00000001011f9754 protectedEval + 36 (context.c:811)
149 libR.dylib                    	0x00000001011f9651 R_ToplevelExec + 625
150 libR.dylib                    	0x00000001011f96fc R_tryEval + 44 (context.c:826)
151 rsession                      	0x00000001007f4167 rstudio::r::exec::(anonymous namespace)::evaluateExpressionsUnsafe(SEXPREC*, SEXPREC*, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::(anonymous namespace)::EvalType) + 407
152 rsession                      	0x00000001007f545e rstudio::r::exec::RFunction::call(SEXPREC*, bool, SEXPREC**, rstudio::r::sexp::Protect*) + 350
153 rsession                      	0x00000001007f5986 rstudio::r::exec::RFunction::call(SEXPREC**, rstudio::r::sexp::Protect*) + 38
154 rsession                      	0x00000001007fa578 rstudio::r::json::(anonymous namespace)::handleRequest(std::string const&, rstudio::core::json::JsonRpcRequest const&, rstudio::core::json::JsonRpcResponse*) + 328
155 rsession                      	0x00000001007fadd2 rstudio_boost::detail::function::function_obj_invoker2<rstudio_boost::_bi::bind_t<rstudio::core::Error, rstudio::core::Error (*)(std::string const&, rstudio::core::json::JsonRpcRequest const&, rstudio::core::json::JsonRpcResponse*), rstudio_boost::_bi::list3<rstudio_boost::_bi::value<std::string>, rstudio_boost::arg<1>, rstudio_boost::arg<2> > >, rstudio::core::Error, rstudio::core::json::JsonRpcRequest const&, rstudio::core::json::JsonRpcResponse*>::invoke(rstudio_boost::detail::function::function_buffer&, rstudio::core::json::JsonRpcRequest const&, rstudio::core::json::JsonRpcResponse*) + 18
156 rsession                      	0x000000010065142e rstudio::core::json::(anonymous namespace)::runSynchronousFunction(rstudio_boost::function<rstudio::core::Error (rstudio::core::json::JsonRpcRequest const&, rstudio::core::json::JsonRpcResponse*)> const&, rstudio::core::json::JsonRpcRequest const&, rstudio_boost::function<void (rstudio::core::Error const&, rstudio::core::json::JsonRpcResponse*)> const&) + 94
157 rsession                      	0x00000001000ef3cf rstudio::session::rpc::handleRpcRequest(rstudio::core::json::JsonRpcRequest const&, rstudio_boost::shared_ptr<rstudio::session::HttpConnection>, rstudio::session::http_methods::ConnectionType) + 991
158 rsession                      	0x00000001000f465c rstudio::session::http_methods::handleConnection(rstudio_boost::shared_ptr<rstudio::session::HttpConnection>, rstudio::session::http_methods::ConnectionType) + 1180
159 rsession                      	0x00000001000f35f7 rstudio::session::http_methods::waitForMethod(std::string const&, rstudio_boost::function<void ()> const&, rstudio_boost::function<bool ()> const&, rstudio::core::json::JsonRpcRequest*) + 2375
160 rsession                      	0x0000000100034339 rstudio::session::console_input::rConsoleRead(std::string const&, bool, rstudio::r::session::RConsoleInput*) + 649
161 rsession                      	0x000000010082abec rstudio::r::session::RReadConsole(char const*, unsigned char*, int, int) + 892
162 libR.dylib                    	0x0000000101280916 Rf_ReplIteration + 86 (main.c:207)
163 libR.dylib                    	0x00000001012821bf run_Rmainloop + 207 (main.c:309)
164 rsession                      	0x00000001008522f9 rstudio::r::session::runEmbeddedR(rstudio::core::FilePath const&, rstudio::core::FilePath const&, bool, bool, SA_TYPE, rstudio::r::session::Callbacks const&, rstudio::r::session::InternalCallbacks*) + 425
165 rsession                      	0x00000001008312fc rstudio::r::session::run(rstudio::r::session::ROptions const&, rstudio::r::session::RCallbacks const&) + 3164
166 rsession                      	0x0000000100109063 main + 28963
167 rsession                      	0x0000000100003cb4 start + 52

*other thread details removed*

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000025fde  rbx: 0x0000000000000000  rcx: 0x00000001113cd668  rdx: 0x0000000000000008
  rdi: 0xffffffffffffffff  rsi: 0x0000000000000000  rbp: 0x00007ffeefbe3640  rsp: 0x00007ffeefbe3630
   r8: 0x0000000000000000   r9: 0x00007ffeefbe3c87  r10: 0x0000000111610910  r11: 0x0000000121b4e41a
  r12: 0x0000000000000000  r13: 0x00000001170b9168  r14: 0x0000000000000020  r15: 0x0000000169aae800
  rip: 0x0000000121cdbd1f  rfl: 0x0000000000000246  cr2: 0x0000000109b2a220
  
Logical CPU:     0
Error Code:      0x020000b8
Trap Number:     133

*binary images removed*

VM Region Summary:
ReadOnly portion of Libraries: Total=472.8M resident=0K(0%) swapped_out_or_unallocated=472.8M(100%)
Writable regions: Total=1.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.5G(100%)
 
                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
ATS (font support)                32.0M        9 
ATS (font support) (reserved)        4K        2         reserved VM address space (unallocated)
Activity Tracing                   256K        2 
Dispatch continuations            8192K        2 
Kernel Alloc Once                    8K        2 
MALLOC                             1.1G      106 
MALLOC guard page                   16K        5 
MALLOC_LARGE (reserved)           15.2M        8         reserved VM address space (unallocated)
STACK GUARD                         68K       16 
Stack                             28.1M       16 
Stack Guard                       56.0M        2 
VM_ALLOCATE                        1.6G       20 
VM_ALLOCATE (reserved)           188.0M        6         reserved VM address space (unallocated)
__DATA                            30.6M      320 
__FONT_DATA                          4K        2 
__LINKEDIT                       244.9M       57 
__TEXT                           227.9M      299 
__UNICODE                          564K        2 
mapped file                       54.2M        9 
shared memory                      648K       10 
===========                     =======  ======= 
TOTAL                              3.6G      875 
TOTAL, minus reserved VM space     3.4G      875

From Troubleshooting Guide: RStudio Crashed

kevinushey · March 26, 2019, 7:12pm

Without a reproducible example it's difficult to say more, but it appears that R is crashing while attempting to initialize Java as through the rJava package.

WillH · March 26, 2019, 7:35pm

Thanks Kevin. I will try and find out why rJava is being called. I didn't think that I even had it loaded.

Will

system · April 16, 2019, 7:36pm

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