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Applied the new astyle to master #1180

Merged
merged 19 commits into from
Jan 17, 2025
+34,637 −16,728

udpated .git-blame-ignore-revs for v2.11

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Merged

Applied the new astyle to master #1180

udpated .git-blame-ignore-revs for v2.11
d628684
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GitHub Advanced Security / CodeQL failed Jan 17, 2025 in 4s

221 new alerts including 4 critical severity security vulnerabilities

New alerts in code changed by this pull request

Security Alerts:

  • 4 critical
  • 29 high

Other Alerts:

  • 6 errors
  • 22 warnings
  • 160 notes

Alerts not introduced by this pull request might have been detected because the code changes were too large.

See annotations below for details.

View all branch alerts.

Annotations

Check notice on line 1094 in src/bias/MetaD.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Equality test on floating-point values Note

Equality checks on floating point values can yield unexpected results.

Check notice on line 683 in src/cltools/Driver.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Declaration hides variable Note

Variable t hides another variable of the same name (on
line 409
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).

Check notice on line 241 in src/cltools/GenJson.cpp

See this annotation in the file changed.

Code scanning / CodeQL

For loop variable changed in body Note

Loop counters should not be modified in the body of the
loop
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.

Check notice on line 344 in src/cltools/ShowGraph.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Unused local variable Note

Variable hasforce is not used.

Check notice on line 271 in src/cltools/pesmd.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Declaration hides variable Note

Variable istep hides another variable of the same name (on
line 255
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).

Check notice on line 281 in src/cltools/pesmd.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Declaration hides variable Note

Variable k hides another variable of the same name (on
line 227
Loading
).

Check notice on line 293 in src/cltools/pesmd.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Declaration hides variable Note

Variable k hides another variable of the same name (on
line 227
Loading
).

Check notice on line 320 in src/cltools/pesmd.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Declaration hides variable Note

Variable k hides another variable of the same name (on
line 227
Loading
).

Check notice on line 332 in src/cltools/pesmd.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Declaration hides variable Note

Variable k hides another variable of the same name (on
line 227
Loading
).

Check notice on line 136 in src/colvar/MultiRMSD.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Declaration hides variable Note

Variable num hides another variable of the same name (on
line 99
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).

Check notice on line 146 in src/colvar/MultiRMSD.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Declaration hides variable Note

Variable num hides another variable of the same name (on
line 99
Loading
).

Check notice on line 183 in src/core/ActionWithMatrix.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Unused local variable Note

Variable outval is not used.

Check failure on line 214 in src/core/ActionWithVector.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Inconsistent nullness check Error

The result of this call to getPntrToAction is not checked for null, but 80% of calls to getPntrToAction check for null.

Check failure on line 231 in src/core/ActionWithVector.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Inconsistent nullness check Error

The result of this call to getPntrToAction is not checked for null, but 80% of calls to getPntrToAction check for null.

Check warning on line 436 in src/core/ActionWithVector.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Local variable address stored in non-local memory Warning

A stack address which arrived via a
parameter
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may be assigned to a non-local variable.

Check notice on line 594 in src/core/ActionWithVector.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Declaration hides variable Note

Variable nt hides another variable of the same name (on
line 560
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).

Check notice on line 80 in src/core/ActionWithVirtualAtom.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Commented-out code Note

This comment appears to contain commented-out code.

Check failure on line 274 in src/core/CLToolMain.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Uncontrolled data used in OS command Critical

This argument to an OS command is derived from
user input (an environment variable)
Loading
, dangerously concatenated into
call to operator+
Loading
, and then passed to system(__command).
This argument to an OS command is derived from
user input (an environment variable)
Loading
, dangerously concatenated into
call to operator+
Loading
, and then passed to system(__command).
This argument to an OS command is derived from
user input (an environment variable)
Loading
, dangerously concatenated into
call to operator+
Loading
, and then passed to system(__command).
This argument to an OS command is derived from
user input (an environment variable)
Loading
, dangerously concatenated into
call to operator+
Loading
, and then passed to system(__command).
This argument to an OS command is derived from
user input (an environment variable)
Loading
, dangerously concatenated into
call to operator+
Loading
, and then passed to system(__command).
This argument to an OS command is derived from
user input (an environment variable)
Loading
, dangerously concatenated into
call to operator+
Loading
, and then passed to system(__command).

Check failure on line 274 in src/core/CLToolMain.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Uncontrolled process operation High

The value of this argument may come from
an environment variable
Loading
and is being passed to system.
The value of this argument may come from
an environment variable
Loading
and is being passed to system.

Check notice on line 165 in src/core/FlexibleBin.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Long switch case Note

Switch has at least one case that is too long:
diffusion (34 lines)
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.

Check notice on line 133 in src/core/FlexibleBin.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Commented-out code Note

This comment appears to contain commented-out code.

Check notice on line 197 in src/core/FlexibleBin.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Commented-out code Note

This comment appears to contain commented-out code.

Check warning on line 74 in src/core/PlumedMain.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Poorly documented large function Warning

Poorly documented function: fewer than 2% comments for a function of 169 lines.

Check notice on line 1204 in src/core/PlumedMain.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Declaration hides variable Note

Variable sw hides another variable of the same name (on
line 1373
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).

Check failure on line 1497 in src/core/PlumedMain.cpp

See this annotation in the file changed.

Code scanning / CodeQL

Uncontrolled data used in OS command Critical

This argument to an OS command is derived from
user input (an environment variable)
Loading
, dangerously concatenated into
call to operator+
Loading
, and then passed to system(__command).
This argument to an OS command is derived from
user input (an environment variable)
Loading
, dangerously concatenated into
call to operator+
Loading
, and then passed to system(__command).
This argument to an OS command is derived from
user input (an environment variable)
Loading
, dangerously concatenated into
call to operator+
Loading
, and then passed to system(__command).
This argument to an OS command is derived from
user input (an environment variable)
Loading
, dangerously concatenated into
call to operator+
Loading
, and then passed to system(__command).
This argument to an OS command is derived from
user input (an environment variable)
Loading
, dangerously concatenated into
call to operator+
Loading
, and then passed to system(__command).
This argument to an OS command is derived from
user input (an environment variable)
Loading
, dangerously concatenated into
call to operator+
Loading
, and then passed to system(__command).