Bug#976505: gkl: FTBFS on arm64: deflate.c:995:36: error: ‘x86_cpu_has_sse42’ undeclared (first use in this function)

Sat Dec 5 12:19:27 GMT 2020

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 at c074c0c
> Creating new cache for resourceHashesCache, path /<<PKGBUILDDIR>>/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess at c074c0c
> Creating new cache for fileHashes, path /<<PKGBUILDDIR>>/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess at 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 at 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 at 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 at 56193c7d
> Creating new cache for taskHistory, path /<<PKGBUILDDIR>>/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess at 64a8d575
> Creating new cache for outputFiles, path /<<PKGBUILDDIR>>/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess at 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 at 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.