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Thu, 6 Feb 2025 15:05:52 GMT (envelope-from git) Date: Thu, 6 Feb 2025 15:05:52 GMT Message-Id: <202502061505.516F5qG3044861@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 041e3a8bc547 - main - biology/gatk: Fix build breakage after gradle update to 8.12.1 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-all@freebsd.org Sender: owner-dev-commits-ports-all@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 041e3a8bc5470fd083f8d20801fe2877e2854cf5 Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=041e3a8bc5470fd083f8d20801fe2877e2854cf5 commit 041e3a8bc5470fd083f8d20801fe2877e2854cf5 Author: Yuri Victorovich AuthorDate: 2025-02-06 08:46:13 +0000 Commit: Yuri Victorovich CommitDate: 2025-02-06 15:05:37 +0000 biology/gatk: Fix build breakage after gradle update to 8.12.1 Reported by: fallout --- biology/gatk/Makefile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/biology/gatk/Makefile b/biology/gatk/Makefile index 2bcf2b0647e3..7a69c6327be0 100644 --- a/biology/gatk/Makefile +++ b/biology/gatk/Makefile @@ -11,7 +11,7 @@ WWW= https://gatk.broadinstitute.org/hc/en-us LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.TXT -BUILD_DEPENDS= gradle:devel/gradle +BUILD_DEPENDS= gradle8:devel/gradle8 RUN_DEPENDS= ${LOCALBASE}/lib/libfml.so:biology/fermi-lite \ gkl>0:biology/gkl \ mummer>0:biology/mummer @@ -106,7 +106,7 @@ post-extract: # need a separate extract step because the cache is in /tmp, and n .endif do-build: - @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle \ + @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle8 \ --gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \ ${GRADLE_ARGS} --build-cache localJar @@ -116,7 +116,7 @@ do-install: do-test: # tests require WITH_LARGE_FILES=ON, and they use a lot of disk space @cd ${WRKSRC} && \ - ${SETENV} ${TEST_ENV} gradle -DLIBBWA_PATH=${PREFIX}/lib/libfml.so test + ${SETENV} ${TEST_ENV} gradle8 -DLIBBWA_PATH=${PREFIX}/lib/libfml.so test # tests results as of version 4.6.1.0: 288552 tests, 301 failures, 37 ignored, 1h55m5.63s duration, 99% successful, see https://github.com/broadinstitute/gatk/issues/8940 # see https://github.com/broadinstitute/gatk/issues/8939: Tests fail to find libgkl libraries in /usr/local/lib