internlm/SWE-Fixer-Train-110K huggingface dataset:
Repository: angr/angr

Issue:
ReachingDefinitionsAnalysis ListIndexError
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Getting an error when I run ReachingDefinitionsAnalysis on some binaries pointing to this line: https://github.com/angr/angr/blob/master/angr/analyses/reaching_definitions/engine_vex.py#L183 

Couple of questions related to this:
- CFGFast MUST be generated before doing a ReachingDefinitionsAnalysis. Should it be this way? This is probably a good assumption but I was using a CFGEmulated. Wondering if this can be changed to just use any CFG that's available?
- this get_all_nodes() function is returning an empty list in my situation and I'm getting a ListIndexError. Could this be because of a decoding/lifting error in my binary - a bunch of these errors print when I load the binary.

For now, I have made the following change in my local version of angr:

```python

function_address = (
self.project.kb
    .cfgs['CFGFast']
    .get_all_nodes(self._codeloc().ins_addr, anyaddr=True)[0]
    .function_address if len(self.project.kb
                             .cfgs['CFGFast']
                             .get_all_nodes(self._codeloc().ins_addr, anyaddr=True)) > 0 else 0
)
```


Discussion:
Hi @swthorn in the past RDA was only CFGFast I believe, but now it appears to support Emulated based on this line: https://github.com/angr/angr/blob/b0f9ec9ba721efc88cf6f29242c902806256b7e0/angr/analyses/reaching_definitions/reaching_definitions.py#L144 

To fix this, we just need to get the most accurate CFG, if I am looking at your code right @Pamplemousse. 

Resolving patch:
diff --git a/angr/analyses/reaching_definitions/engine_vex.py b/angr/analyses/reaching_definitions/engine_vex.py
--- a/angr/analyses/reaching_definitions/engine_vex.py
+++ b/angr/analyses/reaching_definitions/engine_vex.py
@@ -182,7 +182,7 @@ def _store_core(self, addr: Iterable[Union[int,HeapAddress,SpOffset,Undefined]],
                     if isinstance(a, SpOffset):
                         function_address = (
                             self.project.kb
-                                .cfgs['CFGFast']
+                                .cfgs.get_most_accurate()
                                 .get_all_nodes(self._codeloc().ins_addr, anyaddr=True)[0]
                                 .function_address
                         )


Test patch:
Repository: angr/angr

Issue:
Decompilation is not valid when there is double quote in string
If there is a double quote in the string, the generated decompilation will not properly escape the double quotes:

```
    if (v18 == 0)
    {
        sub_4010c0("SetCurrentDirectory("Files")"); /* do not return */
    }
```

where it should be:

```
    if (v15 == 0)
    {
        sub_4010c0("SetCurrentDirectory(\"Files\")"); /* do not return */
    }
```


Discussion:

Resolving patch:
diff --git a/angr/analyses/decompiler/structured_codegen/c.py b/angr/analyses/decompiler/structured_codegen/c.py
--- a/angr/analyses/decompiler/structured_codegen/c.py
+++ b/angr/analyses/decompiler/structured_codegen/c.py
@@ -1434,6 +1434,16 @@ def __init__(self, value, type_, reference_values=None, variable=None, tags: Opt
     def type(self):
         return self._type
 
+    @staticmethod
+    def str_to_c_str(_str):
+        repr_str = repr(_str)
+        base_str = repr_str[1:-1]
+        if repr_str[0] == "'":
+            # check if there's double quotes in the body
+            if '"' in base_str:
+                base_str = base_str.replace('"', '\\"')
+        return f"\"{base_str}\""
+
     def c_repr_chunks(self, indent=0, asexpr=False):
 
         if self.variable is not None:
@@ -1444,7 +1454,7 @@ def c_repr_chunks(self, indent=0, asexpr=False):
                 yield hex(self.reference_values[self._type]), self
             elif isinstance(self._type, SimTypePointer) and isinstance(self._type.pts_to, SimTypeChar):
                 refval = self.reference_values[self._type]  # angr.knowledge_plugin.cfg.MemoryData
-                yield '"' + repr(refval.content.decode('utf-8')).strip("'").strip('"') + '"', self
+                yield CConstant.str_to_c_str(refval.content.decode('utf-8')), self
             else:
                 yield self.reference_values[self.type], self
 


Test patch:
diff --git a/tests/test_decompiler.py b/tests/test_decompiler.py
--- a/tests/test_decompiler.py
+++ b/tests/test_decompiler.py
@@ -466,6 +466,14 @@ def test_decompiling_no_arguments_in_variable_list():
     assert argc_name in code
     assert code.count(argc_name) == 1  # it should only appear once
 
+def test_decompiling_strings_c_representation():
+
+    input_expected = [("""Foo"bar""", "\"Foo\\\"bar\""),
+                      ("""Foo'bar""", "\"Foo'bar\"")]
+
+    for (_input, expected) in input_expected:
+        result = angr.analyses.decompiler.structured_codegen.c.CConstant.str_to_c_str(_input)
+        assert result == expected
 
 def test_decompiling_strings_local_strlen():
     bin_path = os.path.join(test_location, "x86_64", "types", "strings")
Repository: angr/angr

Issue:
MIPS32BE:  stack collided with heap?
Couldn't get to the bottom of this one...

```
#!/home/<user>/angr_pypy/bin/python

import angr
import claripy
import monkeyhex
import logging
import pickle
import time
import sys
import os
import socket
import copy
import argparse
import ipdb

from IPython import embed

proj = angr.Project("httpd", auto_load_libs=False, except_missing_libs=False)

cfg = proj.analyses.CFGFast(normalize=True,
                            fail_fast=True,
                            force_complete_scan=False,
                            data_references=False,
                            cross_references=False,
                            show_progressbar=True)

# some functions we're interested in
funcs = proj.kb.functions
parse_http_req = funcs[0x408f90]

s = proj.factory.blank_state(addr=parse_http_req.addr)

# running it in a simulation manager will allow us to examine the state after it errors out
sm  = proj.factory.simulation_manager(s)
sm.run()

embed()
```
[httpd.zip](https://github.com/angr/angr/files/7671480/httpd.zip)




Discussion:
This issue has been marked as `stale` because it has no recent activity. Please comment or add the `pinned` tag to prevent this issue from being closed.

Resolving patch:
diff --git a/angr/storage/memory_mixins/paged_memory/stack_allocation_mixin.py b/angr/storage/memory_mixins/paged_memory/stack_allocation_mixin.py
--- a/angr/storage/memory_mixins/paged_memory/stack_allocation_mixin.py
+++ b/angr/storage/memory_mixins/paged_memory/stack_allocation_mixin.py
@@ -2,6 +2,7 @@
 
 from .paged_memory_mixin import PagedMemoryMixin
 from ....errors import SimSegfaultException, SimMemoryError
+from ....sim_options import STRICT_PAGE_ACCESS
 
 l = logging.getLogger(__name__)
 
@@ -58,7 +59,7 @@ def allocate_stack_pages(self, addr: int, size: int, **kwargs):
         return result
 
     def _initialize_page(self, pageno: int, **kwargs):
-        if pageno != self._red_pageno:
+        if pageno != self._red_pageno or STRICT_PAGE_ACCESS not in self.state.options:
             return super()._initialize_page(pageno, **kwargs)
 
         return self.allocate_stack_pages((pageno + 1) * self.page_size - 1, self.page_size)[0]


Test patch:
Repository: angr/angr

Issue:
_handle_CmpLT in SimEngineLightVEXMixin did some <= comparision?
### Question

As handler of `CmpLT` in class SimEngineLightVEXMixin (in `angr/engines/light/engine.py`), the code did some `expr_0 <= expr_1` operation. I didn't find any documentation about this. Is it correct?

```py
    def _handle_CmpLT(self, expr):
        args, r = self._binop_get_args(expr)
        if args is None: return r
        expr_0, expr_1 = args

        if self._is_top(expr_0) or self._is_top(expr_1):
            return self._top(1)

        return expr_0 <= expr_1
```


Discussion:

Resolving patch:
diff --git a/angr/engines/light/engine.py b/angr/engines/light/engine.py
--- a/angr/engines/light/engine.py
+++ b/angr/engines/light/engine.py
@@ -704,7 +704,7 @@ def _handle_CmpLT(self, expr):
         if self._is_top(expr_0) or self._is_top(expr_1):
             return self._top(1)
 
-        return expr_0 <= expr_1
+        return expr_0 < expr_1
 
     def _handle_CmpGT(self, expr):
         args, r = self._binop_get_args(expr)


Test patch:
Repository: angr/angr

Issue:
Bug in SimEngineRDVEX: Some memory stores are ignored
### Description

The `if.. elif` construct for handling stores fails to consider addresses which are bitvectors. As a result such stores are ignored and this results in an incomplete dependency graph.

### Steps to reproduce the bug

This binary can be used to reproduce the issue (I compiled it without PIE):
```c
#include <stdio.h>

int global_int = 0;

void main(int argc, char** argv) {
	global_int++;
	return;
}
```

Here is the python script:
```python
#!/usr/bin/env python3
import angr
import angr.analyses.reaching_definitions.dep_graph as dep_graph

path = "/home/schlaf/angr-dev/angr/bug/test_binary"
p = angr.Project(path, auto_load_libs=False)

cfg = p.analyses.CFGFast()

main_fun_addr = 0x00401106
main_fun = cfg.functions.get_by_addr(main_fun_addr)

d = dep_graph.DepGraph()

rd = p.analyses.ReachingDefinitions(subject=main_fun, dep_graph=d, track_calls=True)

graph = d.graph
for e in graph.edges:
    print(e)
```

You can see that an edge, which represents the store to `global_int` is missing.
If we fix this, then `(<Definition {Atom:<Reg 16<8>>, Codeloc:<0x401117 id=0x401106[38] contextless>}>, <Definition {Atom:<Mem 0x404014<4>>, Codeloc:<0x40111a id=0x401106[43] contextless>}>)` appears.

I will open a pull request soon.

### Environment

Your report script does not work for some reason. I confirmed this bug in an angr-dev environment. The last commit on angr is: 71987233ff3fdbb3fa404970a7a56057cbb9ec0d from Nov 7th.

### Additional context

_No response_


Discussion:

Resolving patch:
diff --git a/angr/analyses/reaching_definitions/engine_vex.py b/angr/analyses/reaching_definitions/engine_vex.py
--- a/angr/analyses/reaching_definitions/engine_vex.py
+++ b/angr/analyses/reaching_definitions/engine_vex.py
@@ -218,6 +218,11 @@ def _store_core(self, addr: Iterable[Union[int,HeapAddress,SpOffset]], size: int
                     atom = MemoryLocation(HeapAddress(self.state.get_heap_offset(a)), size)
                     tags = None
 
+                elif isinstance(a, claripy.ast.BV):
+                    addr_v = a._model_concrete.value
+                    atom = MemoryLocation(addr_v, size)
+                    tags = None
+
                 else:
                     continue
 


Test patch:
Repository: angr/angr

Issue:
Duplicate member docs on subclasses
### Description

e.g. the documentation on SimCC's members is also present on SimCCUsercall. This is a huge problem considering that the api docs page is already fucking gigantic, this is just making it multiplicatively bigger.

### Steps to reproduce the bug

_No response_

### Environment

_No response_

### Additional context

_No response_


Discussion:

Resolving patch:
diff --git a/docs/conf.py b/docs/conf.py
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -37,7 +37,6 @@
 autodoc_default_options = {
     "members": True,
     "member-order": "bysource",
-    "inherited-members": True,
     "show-inheritance": True,
     "special-members": "__init__",
     "undoc-members": True,


Test patch:
Repository: angr/angr

Issue:
test_object_identification_x86_64 is broken
### Description
```
======================================================================
FAIL: test_object_identification_x86_64 (__main__.TestFindObjectsStatic.test_object_identification_x86_64)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/matt/work/angr/angr-dev/angr/tests/analyses/test_find_objects_static.py", line 27, in test_object_identification_x86_64
    assert "C" in class_labels
AssertionError
```

Fails 1 in 5 on my machine

### Steps to reproduce the bug

_No response_

### Environment

_No response_

### Additional context

_No response_


Discussion:
Source of non-determinism traced to change in 56fba94d1de158bcf5402105915208995573b0d0 where function manager lookup uses get_by_name, which returns a set of functions

Resolving patch:
diff --git a/angr/knowledge_plugins/functions/function_manager.py b/angr/knowledge_plugins/functions/function_manager.py
--- a/angr/knowledge_plugins/functions/function_manager.py
+++ b/angr/knowledge_plugins/functions/function_manager.py
@@ -1,5 +1,5 @@
 # pylint:disable=raise-missing-from
-from typing import Dict, Set, Optional
+from typing import Dict, Generator, Optional, Set
 import logging
 import collections.abc
 import re
@@ -351,8 +351,10 @@ def __iter__(self):
     def get_by_addr(self, addr) -> Function:
         return self._function_map.get(addr)
 
-    def get_by_name(self, name: str) -> Set[Function]:
-        return {f for f in self._function_map.values() if f.name == name}
+    def get_by_name(self, name: str) -> Generator[Function, None, None]:
+        for f in self._function_map.values():
+            if f.name == name:
+                yield f
 
     def _function_added(self, func: Function):
         """


Test patch:
Repository: angr/angr

Issue:
Comparison operator does not work between OpCode objects
### Description

Getting this error when using angr library functions which use PyPCode.
```
if op.opcode > pypcode.OpCode.RETURN:
E               TypeError: '>' not supported between instances of 'OpCode' and 'OpCode'

../../../.venv/lib/python3.12/site-packages/angr/engines/pcode/lifter.py:898: TypeError
``` 
This works on PyPCode 2.1.0, breaks on 3.0.0.

### Steps to reproduce the bug

_No response_

### Environment

Using python 3.12, newest version of angr, this also fails on older versions of angr as well.

### Additional context

_No response_


Discussion:
Thanks for reporting. I'll fix it.

Resolving patch:
diff --git a/angr/engines/pcode/lifter.py b/angr/engines/pcode/lifter.py
--- a/angr/engines/pcode/lifter.py
+++ b/angr/engines/pcode/lifter.py
@@ -895,10 +895,6 @@ def lift(
             last_decode_addr = irsb.addr
             last_imark_idx = 0
             for op_idx, op in enumerate(irsb._ops):
-                # OpCode space begins with control ops ending with RETURN. Quickly filter non-control instructions.
-                if op.opcode > pypcode.OpCode.RETURN:
-                    continue
-
                 if op.opcode == pypcode.OpCode.IMARK:
                     irsb._instruction_addresses.extend([vn.offset for vn in op.inputs])
                     last_decode_addr = op.inputs[0].offset


Test patch:
Repository: refuel-ai/autolabel

Issue:
[Bug]: Confusing error message when OpenAI API Key is missing
**Describe the bug**
When the OpenAI API key is missing, we see the following error message:

```
File ~/.pyenv/versions/3.8.13/envs/refuel-main/lib/python3.8/site-packages/langchain/load/serializable.py:64, in Serializable.__init__(self, **kwargs)
     63 def __init__(self, **kwargs: Any) -> None:
---> 64     super().__init__(**kwargs)
     65     self._lc_kwargs = kwargs

File ~/.pyenv/versions/3.8.13/envs/refuel-main/lib/python3.8/site-packages/pydantic/main.py:341, in pydantic.main.BaseModel.__init__()

ValidationError: 1 validation error for ChatOpenAI
__root__
  Did not find openai_api_key, please add an environment variable `OPENAI_API_KEY` which contains it, or pass  `openai_api_key` as a named parameter. (type=value_error)
```

This is an error from `langchain`, but `autolabel` doesn't allow passing `openai_api_key` as a named parameter anywhere. 

**To Reproduce**
Call `agent.plan` for a config that uses an OpenAI model without providing the API key as an env variable. 

**Expected behavior**
We should throw an error that simply says that the user should add the API key as an environment variable and not that it should be a named parameter. 


Discussion:

Resolving patch:
diff --git a/src/autolabel/models/openai.py b/src/autolabel/models/openai.py
--- a/src/autolabel/models/openai.py
+++ b/src/autolabel/models/openai.py
@@ -11,6 +11,7 @@
 from autolabel.configs import AutolabelConfig
 from autolabel.cache import BaseCache
 
+import os
 
 logger = logging.getLogger(__name__)
 
@@ -78,6 +79,9 @@ def __init__(self, config: AutolabelConfig, cache: BaseCache = None) -> None:
         # populate model name
         self.model_name = config.model_name() or self.DEFAULT_MODEL
 
+        if os.getenv("OPENAI_API_KEY") == None:
+            raise ValueError("OPENAI_API_KEY environment variable not set")
+
         # populate model params and initialize the LLM
         model_params = config.model_params()
         if config.logit_bias():


Test patch:
Repository: refuel-ai/autolabel

Issue:
[Bug]: Running transforms in Jupyter fails
**Describe the bug**
When running autolabel transforms inside a jupyter notebook, we get the following error:
`asyncio.run() cannot be called from a running event loop`

Since Jupyter runs in an event loop itself, python won't allow running another event loop.

**To Reproduce**
Running WebpageTransform inside a Jupyter notebook will lead to the same error.

**Expected behavior**
There should not be any failure whether running transforms in Jupyter or inside another process.



Discussion:

Resolving patch:
diff --git a/src/autolabel/labeler.py b/src/autolabel/labeler.py
--- a/src/autolabel/labeler.py
+++ b/src/autolabel/labeler.py
@@ -32,6 +32,7 @@
     track,
     track_with_stats,
     gather_async_tasks_with_progress,
+    in_notebook,
 )
 
 console = Console()
@@ -67,6 +68,11 @@ def __init__(
             score_type="logprob_average", llm=self.llm
         )
 
+        if in_notebook():
+            import nest_asyncio
+
+            nest_asyncio.apply()
+
     def run(
         self,
         dataset: AutolabelDataset,
diff --git a/src/autolabel/utils.py b/src/autolabel/utils.py
--- a/src/autolabel/utils.py
+++ b/src/autolabel/utils.py
@@ -364,3 +364,19 @@ def lower(text):
         return text.lower()
 
     return white_space_fix(remove_articles(remove_punc(lower(s))))
+
+
+def in_notebook():
+    """
+    Check if we are in a notebook. Taken from https://stackoverflow.com/a/39662359/9263185
+    """
+    try:
+        from IPython import get_ipython
+
+        if "IPKernelApp" not in get_ipython().config:  # pragma: no cover
+            return False
+    except ImportError:
+        return False
+    except AttributeError:
+        return False
+    return True


Test patch:
Repository: refuel-ai/autolabel

Issue:
[Bug]: labeler.get_confidence_score() chunking codepath references an undefined variable
**Describe the bug**

labeler.get_confidence_score() chunking codepath references an undefined variable. This bug was introduced in https://github.com/refuel-ai/autolabel/commit/be895a758df82d86c99e63977a0570ae132c0dd5


Discussion:

Resolving patch:
diff --git a/src/autolabel/labeler.py b/src/autolabel/labeler.py
--- a/src/autolabel/labeler.py
+++ b/src/autolabel/labeler.py
@@ -314,7 +314,7 @@ def run(
                         if self.config.confidence():
                             try:
                                 annotation.confidence_score = self.get_confidence_score(
-                                    annotation
+                                    annotation, chunk, examples
                                 )
                             except Exception as e:
                                 logger.error(f"Error calculating confidence score: {e}")
@@ -588,7 +588,9 @@ def handle_existing_task_run(
             )
         return task_run
 
-    def get_confidence_score(self, annotation: LLMAnnotation) -> Union[float, dict]:
+    def get_confidence_score(
+        self, annotation: LLMAnnotation, chunk: Dict, examples: List[Dict]
+    ) -> Union[float, dict]:
         full_confidence_input = annotation.confidence_prompt + annotation.raw_response
         if (
             self.llm.returns_token_probs()


Test patch:
Repository: refuel-ai/autolabel

Issue:
[Bug]: CLI doesn't produce an output file
**Describe the bug**
When using the CLI to run an AutoLabel job, no output file is created. There's no mention of how to specify an output file in the CLI documentation and it doesn't look like the CLI implementation supports it.

In some sense this might be a feature request, but it feels like a bug because the CLI is unusable if it doesn't output the labeled data. Please let me know if I'm missing something!

**To Reproduce**
Run any labeling job via CLI and no output file will be created, e.g., 
```bash
autolabel run test_data.csv  autolabel_config.json
```

**Expected behavior**
I would expect an output file with the labeled data.




Discussion:

Resolving patch:
diff --git a/src/autolabel/cli/main.py b/src/autolabel/cli/main.py
--- a/src/autolabel/cli/main.py
+++ b/src/autolabel/cli/main.py
@@ -324,6 +324,9 @@ def run(
     max_items: Annotated[int, typer.Option(help="Max number of items to label")] = None,
     start_index: Annotated[int, typer.Option(help="Index to start at")] = 0,
     cache: Annotated[bool, typer.Option(help="Cache results")] = True,
+    output_name: Annotated[
+        str, typer.Option(help="Path to output file to save run results to")
+    ] = None,
     verbose_debug: Annotated[
         bool, typer.Option("--debug", "-vv", help="Verbose (debug log level)")
     ] = False,
@@ -342,7 +345,9 @@ def run(
     agent = LabelingAgent(config=config, cache=cache)
     config = agent.config
     dataset = AutolabelDataset(dataset, config)
-    agent.run(dataset, max_items=max_items, start_index=start_index)
+    agent.run(
+        dataset, max_items=max_items, output_name=output_name, start_index=start_index
+    )
 
 
 if __name__ == "__main__":


Test patch: