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

Open yurivict opened this issue 1 year ago • 0 comments

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 avatar Aug 04 '24 19:08 yurivict