Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Tests fail to find libgkl libraries in /usr/local/lib #8939

Open
yurivict opened this issue Aug 4, 2024 · 0 comments
Open

Tests fail to find libgkl libraries in /usr/local/lib #8939

yurivict opened this issue Aug 4, 2024 · 0 comments

Comments

@yurivict
Copy link

yurivict commented Aug 4, 2024

Some print messages like this:

Gradle suite > Gradle test > org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanIntelAlignerUnitTest > testSubstringMatchLong[0](359, 7M, SOFTCLIP) STANDARD_ERROR
    03:09:09.419 WARN  NativeLibraryLoader - Unable to load libgkl_utils.so from native/libgkl_utils.so (/tmp/libgkl_utils7398935100372553580.so: Shared object "libm.so.6" not found, required by "libgkl_utils7398935100372553580.so")
Test: Test method testSubstringMatchLong[0](359, 7M, SOFTCLIP)(org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanIntelAlignerUnitTest) produced standard out/err: 03:09:09.419 WARN  IntelSmithWaterman - Intel GKL Utils not loaded

libgkl_utils.so is installed in /usr/local/lib/libgkl_utils.so, which is under the standard prefix location /usr/local where all packages are installed.

OS: FreeBSD 14.1

@yurivict yurivict changed the title Tess fail to find libgkl libraries in /usr/local/lib Tests fail to find libgkl libraries in /usr/local/lib Aug 4, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant