BUG: read_csv giving bus error (sometimes segfault too)

[Droidking18]

Pandas version checks

• I have checked that this issue has not already been reported.

• I have confirmed this bug exists on the latest version of pandas.

• I have confirmed this bug exists on the main branch of pandas.

Reproducible Example

import pandas as pd

def main():

    group = pd.DataFrame({'code': [ 'group_value' ]})

    test = pd.read_csv('./test_csv_2.csv')

    # If this line is used instead of read_csv, no issues
    # test = pd.DataFrame({'run_number': [20], 'group': ['group_code'], 'test': ['NaN'], 'test1': ['NaN'], 'test2': ['NaN'], 'test3': ['NaN'], 'test4': ['NaN'], 'test5': ['NaN']})

    newDf = pd.DataFrame().reindex_like(test)

    newDf['group'] = group['code']

    newDf.columns.values[5:7] = ['curr', 'comp']

    print(newDf)

main()

Issue Description

When running the given code, I sometimes run into a bus error:

See:

Bus Error

Fatal Python error: Bus error

Current thread 0x00000001e26c8100 (most recent call first):
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/core/indexes/base.py", line 5010 in __contains__
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/format.py", line 907 in _get_formatter
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/format.py", line 946 in <listcomp>
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/format.py", line 945 in _get_formatted_column_labels
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/format.py", line 864 in _get_strcols_without_index
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/format.py", line 611 in get_strcols
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/string.py", line 31 in _get_strcols
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/string.py", line 40 in _get_string_representation
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/string.py", line 25 in to_string
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/format.py", line 1128 in to_string
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/core/frame.py", line 1192 in to_string
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/core/frame.py", line 1011 in __repr__
  File "/Users/dovikaplan/pandas_crash_test/Basys Files/Remaining CSV files.py", line 21 in main
  File "/Users/dovikaplan/pandas_crash_test/Basys Files/Remaining CSV files.py", line 23 in <module>

Extension modules: numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.strptime, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.tslib, pandas._libs.lib, pandas._libs.hashing, pandas._libs.ops, pandas._libs.arrays, pandas._libs.index, pandas._libs.join, pandas._libs.sparse, pandas._libs.reduction, pandas._libs.indexing, pandas._libs.internals, pandas._libs.writers, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.testing, pandas._libs.parsers, pandas._libs.json (total: 54)
zsh: bus error  python3.10 Remaining\ CSV\ files.py

and

Seg Fault

Fatal Python error: Segmentation fault

Current thread 0x00000001e26c8100 (most recent call first):
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/core/indexes/base.py", line 5291 in __contains__
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/format.py", line 915 in _get_formatter
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/format.py", line 954 in <listcomp>
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/format.py", line 953 in _get_formatted_column_labels
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/format.py", line 872 in _get_strcols_without_index
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/format.py", line 617 in get_strcols
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/string.py", line 36 in _get_strcols
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/string.py", line 45 in _get_string_representation
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/string.py", line 30 in to_string
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/io/formats/format.py", line 1136 in to_string
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/core/frame.py", line 1245 in to_string
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pandas/core/frame.py", line 1064 in __repr__
  File "/Users/dovikaplan/pandas_crash_test/Basys Files/Remaining CSV files.py", line 21 in main
  File "/Users/dovikaplan/pandas_crash_test/Basys Files/Remaining CSV files.py", line 23 in <module>

Extension modules: numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.tslib, pandas._libs.lib, pandas._libs.hashing, pandas._libs.ops, pandas._libs.arrays, pandas._libs.index, pandas._libs.join, pandas._libs.sparse, pandas._libs.reduction, pandas._libs.indexing, pandas._libs.internals, pandas._libs.writers, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.tslibs.strptime, pandas._libs.groupby, pandas._libs.testing, pandas._libs.parsers, pandas._libs.json (total: 54)
zsh: segmentation fault  python3.10 Remaining\ CSV\ files.py

Occasionally, however, it does work, but other times I get a segfault.

The contents of the csv file I import is:

run_number,group,test,test2,test3,test4,test5
20,group_value,,,,,

If I uncomment the line that manually creates the df, instead of pulling from csv, I get no issues, so I'm thinking that where the issue comes from.

Expected Behavior

No segfault or bus errors

Installed Versions

commit : 2e218d1
python : 3.10.4.final.0
python-bits : 64
OS : Darwin
OS-release : 22.3.0
Version : Darwin Kernel Version 22.3.0: Thu Jan 5 20:48:54 PST 2023; root:xnu-8792.81.2~2/RELEASE_ARM64_T6000
machine : arm64
processor : arm
byteorder : little
LC_ALL : None
LANG : en_GB.UTF-8
LOCALE : None.UTF-8

pandas : 1.5.3
numpy : 1.23.1
pytz : 2022.1
dateutil : 2.8.2
setuptools : 58.1.0
pip : 22.3.1
Cython : None
pytest : None
hypothesis : None
sphinx : None
blosc : None
feather : None
xlsxwriter : None
lxml.etree : None
html5lib : None
pymysql : None
psycopg2 : None
jinja2 : 3.1.2
IPython : 8.5.0
pandas_datareader: None
bs4 : 4.11.1
bottleneck : None
brotli : None
fastparquet : None
fsspec : None
gcsfs : None
matplotlib : 3.6.2
numba : None
numexpr : None
odfpy : None
openpyxl : 3.0.10
pandas_gbq : None
pyarrow : None
pyreadstat : None
pyxlsb : None
s3fs : None
scipy : 1.9.3
snappy : None
sqlalchemy : None
tables : None
tabulate : 0.8.10
xarray : None
xlrd : None
xlwt : None
zstandard : None
tzdata : None

[phofl]

Hi, thanks for your report. Can reproduce on 1.5.3 but not on main. Could you try on the rc for 2.0 as well?

[Droidking18]

Thank you, tested on 2.0.0 rc as well as 2.1.0.dev0+119.gb3913977ee. Can reproduce on both my end

[Droidking18]

Just to add in, sometimes I can run it quite a few times before it actually segfaults/bus errors, other times it errors out right away

[phofl]

Running it a couple of times reproduces for me as well. In general, what you are doing with your columns isn't recommended. An Index is considered immutable, hence this can get weird, meaning updating the underlying array