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torognes / swarm

A robust and fast clustering method for amplicon-based studies
GNU Affero General Public License v3.0
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Potential vulnerabilities identified by Flawfinder #115

Closed frederic-mahe closed 5 years ago

frederic-mahe commented 6 years ago

This is a low-priority issue.

while looking at the static code analysis functionalities offered by gitlab, I learned about flawfinder. It is a simple tool mostly focusing on C/C++ functions that are known to be vulnerable, but it can help us spot potential problems in our code, especially for sections dealing with user input (files and command arguments). The vulnerabilities are listed by decreasing importance (nothing major here):

Flawfinder version 2.0.6, (C) 2001-2017 David A. Wheeler.
Number of rules (primarily dangerous function names) in C/C++ ruleset: 223
Examining swarm/src/bitmap.h
Examining swarm/src/ssse3.cc
Examining swarm/src/search8.cc
Examining swarm/src/derep.cc
Examining swarm/src/qgram.cc
Examining swarm/src/nw.cc
Examining swarm/src/util.cc
Examining swarm/src/arch.cc
Examining swarm/src/matrix.cc
Examining swarm/src/algod1.cc
Examining swarm/src/threads.h
Examining swarm/src/swarm.cc
Examining swarm/src/db.cc
Examining swarm/src/search16.cc
Examining swarm/src/algo.cc
Examining swarm/src/bloom.h
Examining swarm/src/scan.cc
Examining swarm/src/cityhash/city.cc
Examining swarm/src/cityhash/config.h
Examining swarm/src/cityhash/citycrc.h
Examining swarm/src/cityhash/city.h
Examining swarm/src/swarm.h
Warning: Skipping directory with initial dot swarm/.git

FINAL RESULTS:

swarm/src/util.cc:84:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
swarm/src/swarm.cc:331:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
swarm/src/algod1.cc:316:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/algod1.cc:337:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/algod1.cc:339:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/algod1.cc:350:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/algod1.cc:351:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/algod1.cc:717:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/algod1.cc:734:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/algod1.cc:746:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/algod1.cc:781:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/algod1.cc:798:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/algod1.cc:810:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/algod1.cc:851:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/algod1.cc:872:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/algod1.cc:888:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/cityhash/city.cc:40:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/cityhash/city.cc:46:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/cityhash/city.cc:591:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
swarm/src/cityhash/city.cc:592:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/db.cc:32:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
swarm/src/db.cc:52:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
swarm/src/db.cc:184:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
swarm/src/db.cc:203:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
swarm/src/db.cc:238:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/db.cc:249:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/db.cc:406:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
swarm/src/db.cc:666:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
swarm/src/derep.cc:61:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
swarm/src/nw.cc:35:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
swarm/src/nw.cc:36:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
swarm/src/nw.cc:38:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/nw.cc:52:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
swarm/src/nw.cc:53:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
swarm/src/nw.cc:55:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
swarm/src/search8.cc:52:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
swarm/src/swarm.cc:571:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
swarm/src/swarm.cc:580:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
swarm/src/swarm.cc:589:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
swarm/src/swarm.cc:598:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
swarm/src/swarm.cc:607:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
swarm/src/swarm.cc:616:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
swarm/src/swarm.h:85:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
swarm/src/db.cc:223:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
swarm/src/db.cc:395:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
swarm/src/db.cc:400:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).

ANALYSIS SUMMARY:

Hits = 46
Lines analyzed = 8676 in approximately 0.13 seconds (67417 lines/second)
Physical Source Lines of Code (SLOC) = 6329
Hits@level = [0] 267 [1]   3 [2]  41 [3]   1 [4]   1 [5]   0
Hits@level+ = [0+] 313 [1+]  46 [2+]  43 [3+]   2 [4+]   1 [5+]   0
Hits/KSLOC@level+ = [0+] 49.4549 [1+] 7.26813 [2+] 6.79412 [3+] 0.316006 [4+] 0.158003 [5+]   0
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://www.dwheeler.com/secure-programs) for more information.
frederic-mahe commented 5 years ago

@torognes could you please give a look at the above list? It contains general advice, and I don't think there is anything specific that could be applied to swarm's code. Please close the issue when you are done.

torognes commented 5 years ago

I've gone through the list and considered each issue and looked at the code. As far as I can see none of the issues are real problems in Swarm as the potential problems are taken care of in the code (array sizes, length of strings and memory areas). I have made a small change by replacing a sprintf call with a snprintf call, even though I can't see how it should break.