Source: gkl Version: 0.8.6+dfsg-2 Severity: important Justification: FTBFS on arm64 Tags: bullseye sid ftbfs Usertags: ftbfs-20201205 ftbfs-bullseye
Hi, During a rebuild of all packages in sid, your package failed to build on arm64. Relevant part (hopefully): > make[1]: Entering directory '/<<PKGBUILDDIR>>' > dh_auto_build -- jar > mkdir -p .gradle/init.d > cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ > gradle --info --console plain --offline --stacktrace --no-daemon > --refresh-dependencies --gradle-user-home .gradle -Duser.home=. > -Duser.name=debian -Ddebian.package=gkl -Dfile.encoding=UTF-8 --parallel > --max-workers=4 jar > Initialized native services in: /<<PKGBUILDDIR>>/.gradle/native > Using 4 worker leases. > Creating new cache for fileHashes, path > /<<PKGBUILDDIR>>/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access > org.gradle.cache.internal.DefaultCacheAccess@c074c0c > Creating new cache for resourceHashesCache, path > /<<PKGBUILDDIR>>/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, > access org.gradle.cache.internal.DefaultCacheAccess@c074c0c > Creating new cache for fileHashes, path > /<<PKGBUILDDIR>>/.gradle/4.4.1/fileHashes/fileHashes.bin, access > org.gradle.cache.internal.DefaultCacheAccess@56193c7d > WARNING: An illegal reflective access operation has occurred > WARNING: Illegal reflective access using Lookup on > org.gradle.internal.reflect.JavaMethod > (file:/usr/share/gradle/lib/gradle-base-services-4.4.1.jar) to class > java.lang.ClassLoader > WARNING: Please consider reporting this to the maintainers of > org.gradle.internal.reflect.JavaMethod > WARNING: Use --illegal-access=warn to enable warnings of further illegal > reflective access operations > WARNING: All illegal access operations will be denied in a future release > Starting Build > Compiling initialization script '/<<PKGBUILDDIR>>/.gradle/init.d/init.gradle' > using SubsetScriptTransformer. > Creating new cache for metadata-1.1/results, path > /<<PKGBUILDDIR>>/.gradle/caches/transforms-1/metadata-1.1/results.bin, access > org.gradle.cache.internal.DefaultCacheAccess@5dc769f9 > Compiling initialization script '/<<PKGBUILDDIR>>/.gradle/init.d/init.gradle' > using BuildScriptTransformer. > Settings evaluated using settings file '/<<PKGBUILDDIR>>/settings.gradle'. > Settings file not found (/<<PKGBUILDDIR>>/settings.gradle) > Root project name not defined in settings.gradle, defaulting to 'gkl' > instead of the name of the root directory 'gkl-0.8.6+dfsg' > Projects loaded. Root project using build file > '/<<PKGBUILDDIR>>/build.gradle'. > Included projects: [root project 'gkl'] > Keep-alive timer started > Adding Debian repository to project 'gkl' > Parallel execution is an incubating feature. > Evaluating root project 'gkl' using build file > '/<<PKGBUILDDIR>>/build.gradle'. > Compiling build file '/<<PKGBUILDDIR>>/build.gradle' using > SubsetScriptTransformer. > Compiling build file '/<<PKGBUILDDIR>>/build.gradle' using > BuildScriptTransformer. > Starting process 'command 'dpkg-parsechangelog''. Working directory: > /<<PKGBUILDDIR>> Command: dpkg-parsechangelog -S Version > Successfully started process 'command 'dpkg-parsechangelog'' > Adding Maven pom generation to project 'gkl' > Linking the generated javadoc to the system JDK API documentation > All projects evaluated. > Selected primary task 'jar' from project : > Creating new cache for annotation-processors, path > /<<PKGBUILDDIR>>/.gradle/4.4.1/fileContent/annotation-processors.bin, access > org.gradle.cache.internal.DefaultCacheAccess@4fc256ec > Tasks to be executed: [task ':compileJava', task ':cmakeConfig', task > ':cmakeBuild', task ':copyNativeLib', task ':buildOnMac', task > ':processResources', task ':classes', task ':debianMavenPom', task ':jar'] > Creating new cache for resourceHashesCache, path > /<<PKGBUILDDIR>>/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access > org.gradle.cache.internal.DefaultCacheAccess@56193c7d > Creating new cache for taskHistory, path > /<<PKGBUILDDIR>>/.gradle/4.4.1/taskHistory/taskHistory.bin, access > org.gradle.cache.internal.DefaultCacheAccess@64a8d575 > Creating new cache for outputFiles, path > /<<PKGBUILDDIR>>/.gradle/buildOutputCleanup/outputFiles.bin, access > org.gradle.cache.internal.DefaultCacheAccess@35cf91df > :compileJava (Thread[Task worker for ':',5,main]) started. > :compileJava > Putting task artifact state for task ':compileJava' into context took 0.003 > secs. > Creating new cache for metadata-2.36/module-metadata, path > /<<PKGBUILDDIR>>/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, > access org.gradle.cache.internal.DefaultCacheAccess@27a444be > Loading the Maven rules... > Replacing commons-io:commons-io:jar:2.4 -> > commons-io:commons-io:jar:debian > Passing through org.apache.commons:commons-parent:jar:debian > Passing through org.apache:apache:jar:debian > Passing through org.broadinstitute:gatk-native-bindings:jar:debian > Replacing org.apache.logging.log4j:log4j-api:jar:2.5 -> > org.apache.logging.log4j:log4j-api:jar:debian > Passing through org.apache.logging.log4j:log4j:jar:debian > Replacing org.apache.logging.log4j:log4j-core:jar:2.5 -> > org.apache.logging.log4j:log4j-core:jar:debian > Replacing com.github.samtools:htsjdk:jar:2.9.0 -> > com.github.samtools:htsjdk:jar:debian > Passing through org.apache.commons:commons-jexl:jar:debian > Passing through commons-logging:commons-logging:jar:debian > Passing through org.xerial.snappy:snappy-java:jar:debian > Passing through org.apache.commons:commons-compress:jar:debian > Passing through org.tukaani:xz:jar:debian > Passing through gov.nih.nlm.ncbi:ngs-java:jar:debian > Up-to-date check for task ':compileJava' took 0.793 secs. It is not > up-to-date because: > No history is available. > All input files are considered out-of-date for incremental task > ':compileJava'. > Compiling with JDK Java compiler API. > :compileJava (Thread[Task worker for ':',5,main]) completed. Took 1.633 secs. > :cmakeConfig (Thread[Task worker for ':',5,main]) started. > :cmakeConfig > Putting task artifact state for task ':cmakeConfig' into context took 0.0 > secs. > Up-to-date check for task ':cmakeConfig' took 0.046 secs. It is not > up-to-date because: > No history is available. > Starting process 'command 'cmake''. Working directory: > /<<PKGBUILDDIR>>/build/native Command: cmake -Wno-dev /<<PKGBUILDDIR>> > Successfully started process 'command 'cmake'' > :cmakeConfig (Thread[Task worker for ':',5,main]) completed. Took 0.931 secs. > :cmakeBuild (Thread[Task worker for ':',5,main]) started. > :cmakeBuild > Putting task artifact state for task ':cmakeBuild' into context took 0.002 > secs. > Up-to-date check for task ':cmakeBuild' took 0.0 secs. It is not up-to-date > because: > Task.upToDateWhen is false. > Starting process 'command 'make''. Working directory: > /<<PKGBUILDDIR>>/build/native Command: make install > Successfully started process 'command 'make'' > /<<PKGBUILDDIR>>/build/native/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c: > In function ‘deflate’: > /<<PKGBUILDDIR>>/build/native/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:995:36: > error: ‘x86_cpu_has_sse42’ undeclared (first use in this function) > 995 | else if (s->level == 1 && !x86_cpu_has_sse42) > | ^~~~~~~~~~~~~~~~~ > /<<PKGBUILDDIR>>/build/native/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:995:36: > note: each undeclared identifier is reported only once for each function it > appears in > make[5]: *** [Makefile:197: deflate.o] Error 1 The full build log is available from: http://qa-logs.debian.net/2020/12/05/gkl_0.8.6+dfsg-2_unstable.log A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! If you reassign this bug to another package, please marking it as 'affects'-ing this package. See https://www.debian.org/Bugs/server-control#affects If you fail to reproduce this, please provide a build log and diff it with me so that we can identify if something relevant changed in the meantime. About the archive rebuild: The rebuild was done on EC2 VM instances from Amazon Web Services, using a clean, minimal and up-to-date chroot. Every failed build was retried once to eliminate random failures.
