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Update docker images to reduce security vulnerabilities #211

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Update docker images to reduce security vulnerabilities #211

chore: add --verbose flag to tests
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GitHub Advanced Security / Snyk Container failed Jan 31, 2025 in 1s

8 configurations not found

Warning: Code scanning may not have found all the alerts introduced by this pull request, because 8 configurations present on refs/heads/main were not found:

Actions workflow (docker-build.yaml)

  • ❓  .github/workflows/docker-build.yaml:build-images/image:docker/bwa
  • ❓  .github/workflows/docker-build.yaml:build-images/image:docker/estimate
  • ❓  .github/workflows/docker-build.yaml:build-images/image:docker/minfi
  • ❓  .github/workflows/docker-build.yaml:build-images/image:docker/pandas
  • ❓  .github/workflows/docker-build.yaml:build-images/image:docker/python-plotting
  • ❓  .github/workflows/docker-build.yaml:build-images/image:docker/star
  • ❓  .github/workflows/docker-build.yaml:build-images/image:docker/umap
  • ❓  .github/workflows/docker-build.yaml:build-images/image:docker/util

New alerts in code changed by this pull request

Security Alerts:

  • 3 high
  • 9 medium
  • 1 low

Other Alerts:

  • 7 warnings
  • 5 notes

See annotations below for details.

View all branch alerts.

Annotations

Check warning on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Low severity - Allocation of Resources Without Limits or Throttling vulnerability in binutils Medium

This file introduces a vulnerable binutils package with a low severity vulnerability.

Check warning on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Low severity - Improper Input Validation vulnerability in coreutils Medium

This file introduces a vulnerable coreutils package with a low severity vulnerability.

Check warning on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - Integer Overflow or Wraparound vulnerability in freetype Medium

This file introduces a vulnerable freetype package with a medium severity vulnerability.

Check failure on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Low severity - Allocation of Resources Without Limits or Throttling vulnerability in glibc High

This file introduces a vulnerable glibc package with a low severity vulnerability.

Check notice on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Low severity - Out-of-bounds Write vulnerability in gnupg2 Low

This file introduces a vulnerable gnupg2 package with a low severity vulnerability.

Check warning on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Low severity - Race Condition vulnerability in htslib Medium

This file introduces a vulnerable htslib package with a low severity vulnerability.

Check notice on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Low severity - CVE-2024-26458 vulnerability in krb5 Note

This file introduces a vulnerable krb5 package with a low severity vulnerability.

Check warning on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2024-26462 vulnerability in krb5 Warning

This file introduces a vulnerable krb5 package with a medium severity vulnerability.

Check notice on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Low severity - CVE-2024-26461 vulnerability in krb5 Note

This file introduces a vulnerable krb5 package with a low severity vulnerability.

Check warning on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2024-38949 vulnerability in libde265 Warning

This file introduces a vulnerable libde265 package with a medium severity vulnerability.

Check warning on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2024-38950 vulnerability in libde265 Warning

This file introduces a vulnerable libde265 package with a medium severity vulnerability.

Check notice on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Low severity - Information Exposure vulnerability in libgcrypt20 Note

This file introduces a vulnerable libgcrypt20 package with a low severity vulnerability.

Check warning on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Low severity - NULL Pointer Dereference vulnerability in libpng1.6 Medium

This file introduces a vulnerable libpng1.6 package with a low severity vulnerability.

Check warning on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Low severity - Allocation of Resources Without Limits or Throttling vulnerability in openjpeg2 Medium

This file introduces a vulnerable openjpeg2 package with a low severity vulnerability.

Check warning on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - Resource Exhaustion vulnerability in openjpeg2 Warning

This file introduces a vulnerable openjpeg2 package with a medium severity vulnerability.

Check warning on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - Resource Exhaustion vulnerability in openjpeg2 Warning

This file introduces a vulnerable openjpeg2 package with a medium severity vulnerability.

Check notice on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Low severity - CVE-2024-41996 vulnerability in openssl Note

This file introduces a vulnerable openssl package with a low severity vulnerability.

Check warning on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - Insecure Storage of Sensitive Information vulnerability in pam Medium

This file introduces a vulnerable pam package with a medium severity vulnerability.

Check failure on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - Improper Authentication vulnerability in pam High

This file introduces a vulnerable pam package with a medium severity vulnerability.

Check warning on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Low severity - Release of Invalid Pointer or Reference vulnerability in patch Medium

This file introduces a vulnerable patch package with a low severity vulnerability.

Check failure on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Low severity - Double Free vulnerability in patch High

This file introduces a vulnerable patch package with a low severity vulnerability.

Check warning on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2024-35195 vulnerability in python-pip Warning

This file introduces a vulnerable python-pip package with a medium severity vulnerability.

Check warning on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2024-56433 vulnerability in shadow Warning

This file introduces a vulnerable shadow package with a medium severity vulnerability.

Check notice on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Low severity - CVE-2024-6716 vulnerability in tiff Note

This file introduces a vulnerable tiff package with a low severity vulnerability.

Check warning on line 1 in docker/util/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - Open Redirect vulnerability in wget Medium

This file introduces a vulnerable wget package with a medium severity vulnerability.