Continued build issues with IGV: Could not resolve org.apache.logging.log4j:log4j:debian

[Andreas Tille]

Hi Olivier,

thanks a lot for looking into this.

sorry for the private ping, but may be you have an idea how to
build igv?

Hi,
after lots of fixes, I could get igv build (and had to make a few
updates to d/bin/igv too)
however, I removed the Java 9 module support for igv itself.. Could not
make it build to provide igv as a module, only as a "old" lib/bin
could not test due to x11 pb, but it builds and do not complain on
missing libs.
I pushed all my updates

I tried to build your latest commit (eaa95f1c [1]) but I get:

...
Passing through xalan:serializer:jar:debian
Passing through commons-logging:commons-logging:jar:debian
:compileJava FAILED
:compileJava (Thread[Daemon worker,5,main]) completed. Took 0.64 secs.

FAILURE: Build failed with an exception.

* What went wrong:
Could not resolve all files for configuration ':compileClasspath'.

Could not resolve org.apache.logging.log4j:log4j:debian.
No cached version of org.apache.logging.log4j:log4j:debian available for offline mode.
Could not resolve org.apache.logging.log4j:log4j-api:debian.
No cached version of org.apache.logging.log4j:log4j-api:debian available for offline mode.
Could not resolve org.apache.logging.log4j:log4j-1.2-api:debian.
No cached version of org.apache.logging.log4j:log4j-1.2-api:debian available for offline mode.
Could not resolve org.apache.logging.log4j:log4j-core:debian.
No cached version of org.apache.logging.log4j:log4j-core:debian available for offline mode.

* Try:
Run with --debug option to get more log output. Run with --scan to get full insights.

* Exception is:
org.gradle.api.internal.artifacts.ivyservice.DefaultLenientConfiguration$ArtifactResolveException: Could not resolve all files for configuration ':compileClasspath'.
at org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.rethrowFailure(DefaultConfiguration.java:918)
at org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.access$1600(DefaultConfiguration.java:116)
at org.gradle.api.internal.artifacts.configurations.DefaultConfiguration$ConfigurationFileCollection.getFiles(DefaultConfiguration.java:892)
at org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.getFiles(DefaultConfiguration.java:404)
...
at org.gradle.api.internal.artifacts.ivyservice.ivyresolve.ComponentMetaDataResolveState.resolve(ComponentMetaDataResolveState.java:58)
at org.gradle.api.internal.artifacts.ivyservice.ivyresolve.RepositoryChainComponentMetaDataResolver.findBestMatch(RepositoryChainComponentMetaDataResolver.java:138)
at org.gradle.api.internal.artifacts.ivyservice.ivyresolve.RepositoryChainComponentMetaDataResolver.findBestMatch(RepositoryChainComponentMetaDataResolver.java:119)
at org.gradle.api.internal.artifacts.ivyservice.ivyresolve.RepositoryChainComponentMetaDataResolver.resolveModule(RepositoryChainComponentMetaDataResolver.java:92)
... 143 more


* Get more help at https://help.gradle.org

BUILD FAILED in 7s
1 actionable task: 1 executed
dh_auto_build: gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=igv -Dfile.encoding=UTF-8 --parallel --max-workers=4 jar returned exit code 1


in a recent pbuilder chroot.

I would love to test igv, but it seems it does not build reliably. :-(

Kind regards

Andreas.


[1] https://salsa.debian.org/med-team/igv/commit/eaa95f1c5d56003c91984f1e2036bbf8bae7fec0

[Olivier Sallou]

Post by Andreas Tille
Hi Olivier,
thanks a lot for looking into this.

sorry for the private ping, but may be you have an idea how to
build igv?

Hi,
after lots of fixes, I could get igv build (and had to make a few
updates to d/bin/igv too)
however, I removed the Java 9 module support for igv itself.. Could not
make it build to provide igv as a module, only as a "old" lib/bin
could not test due to x11 pb, but it builds and do not complain on
missing libs.
I pushed all my updates

...
Passing through xalan:serializer:jar:debian
Passing through commons-logging:commons-logging:jar:debian
:compileJava FAILED
:compileJava (Thread[Daemon worker,5,main]) completed. Took 0.64 secs.
FAILURE: Build failed with an exception.
Could not resolve all files for configuration ':compileClasspath'.

Could not resolve org.apache.logging.log4j:log4j:debian.

certainly some missing deps.... I gonna check

Post by Andreas Tille

No cached version of org.apache.logging.log4j:log4j:debian available for offline mode.
Could not resolve org.apache.logging.log4j:log4j-api:debian.
No cached version of org.apache.logging.log4j:log4j-api:debian available for offline mode.
Could not resolve org.apache.logging.log4j:log4j-1.2-api:debian.
No cached version of org.apache.logging.log4j:log4j-1.2-api:debian available for offline mode.
Could not resolve org.apache.logging.log4j:log4j-core:debian.
No cached version of org.apache.logging.log4j:log4j-core:debian available for offline mode.

Run with --debug option to get more log output. Run with --scan to get full insights.
org.gradle.api.internal.artifacts.ivyservice.DefaultLenientConfiguration$ArtifactResolveException: Could not resolve all files for configuration ':compileClasspath'.
at org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.rethrowFailure(DefaultConfiguration.java:918)
at org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.access$1600(DefaultConfiguration.java:116)
at org.gradle.api.internal.artifacts.configurations.DefaultConfiguration$ConfigurationFileCollection.getFiles(DefaultConfiguration.java:892)
at org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.getFiles(DefaultConfiguration.java:404)
...
at org.gradle.api.internal.artifacts.ivyservice.ivyresolve.ComponentMetaDataResolveState.resolve(ComponentMetaDataResolveState.java:58)
at org.gradle.api.internal.artifacts.ivyservice.ivyresolve.RepositoryChainComponentMetaDataResolver.findBestMatch(RepositoryChainComponentMetaDataResolver.java:138)
at org.gradle.api.internal.artifacts.ivyservice.ivyresolve.RepositoryChainComponentMetaDataResolver.findBestMatch(RepositoryChainComponentMetaDataResolver.java:119)
at org.gradle.api.internal.artifacts.ivyservice.ivyresolve.RepositoryChainComponentMetaDataResolver.resolveModule(RepositoryChainComponentMetaDataResolver.java:92)
... 143 more
* Get more help at https://help.gradle.org
BUILD FAILED in 7s
1 actionable task: 1 executed
dh_auto_build: gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=igv -Dfile.encoding=UTF-8 --parallel --max-workers=4 jar returned exit code 1
in a recent pbuilder chroot.
I would love to test igv, but it seems it does not build reliably. :-(
Kind regards
Andreas.
[1] https://salsa.debian.org/med-team/igv/commit/eaa95f1c5d56003c91984f1e2036bbf8bae7fec0

[Olivier Sallou]

Post by Andreas Tille
Hi Olivier,
thanks a lot for looking into this.

I pushed missing d/control dep liblog4j2-java

Post by Andreas Tille

sorry for the private ping, but may be you have an idea how to
build igv?

Hi,
after lots of fixes, I could get igv build (and had to make a few
updates to d/bin/igv too)
however, I removed the Java 9 module support for igv itself.. Could not
make it build to provide igv as a module, only as a "old" lib/bin
could not test due to x11 pb, but it builds and do not complain on
missing libs.
I pushed all my updates

...
Passing through xalan:serializer:jar:debian
Passing through commons-logging:commons-logging:jar:debian
:compileJava FAILED
:compileJava (Thread[Daemon worker,5,main]) completed. Took 0.64 secs.
FAILURE: Build failed with an exception.
Could not resolve all files for configuration ':compileClasspath'.

Could not resolve org.apache.logging.log4j:log4j:debian.
No cached version of org.apache.logging.log4j:log4j:debian available for offline mode.
Could not resolve org.apache.logging.log4j:log4j-api:debian.
No cached version of org.apache.logging.log4j:log4j-api:debian available for offline mode.
Could not resolve org.apache.logging.log4j:log4j-1.2-api:debian.
No cached version of org.apache.logging.log4j:log4j-1.2-api:debian available for offline mode.
Could not resolve org.apache.logging.log4j:log4j-core:debian.
No cached version of org.apache.logging.log4j:log4j-core:debian available for offline mode.

Run with --debug option to get more log output. Run with --scan to get full insights.
org.gradle.api.internal.artifacts.ivyservice.DefaultLenientConfiguration$ArtifactResolveException: Could not resolve all files for configuration ':compileClasspath'.
at org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.rethrowFailure(DefaultConfiguration.java:918)
at org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.access$1600(DefaultConfiguration.java:116)
at org.gradle.api.internal.artifacts.configurations.DefaultConfiguration$ConfigurationFileCollection.getFiles(DefaultConfiguration.java:892)
at org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.getFiles(DefaultConfiguration.java:404)
...
at org.gradle.api.internal.artifacts.ivyservice.ivyresolve.ComponentMetaDataResolveState.resolve(ComponentMetaDataResolveState.java:58)
at org.gradle.api.internal.artifacts.ivyservice.ivyresolve.RepositoryChainComponentMetaDataResolver.findBestMatch(RepositoryChainComponentMetaDataResolver.java:138)
at org.gradle.api.internal.artifacts.ivyservice.ivyresolve.RepositoryChainComponentMetaDataResolver.findBestMatch(RepositoryChainComponentMetaDataResolver.java:119)
at org.gradle.api.internal.artifacts.ivyservice.ivyresolve.RepositoryChainComponentMetaDataResolver.resolveModule(RepositoryChainComponentMetaDataResolver.java:92)
... 143 more
* Get more help at https://help.gradle.org
BUILD FAILED in 7s
1 actionable task: 1 executed
dh_auto_build: gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=igv -Dfile.encoding=UTF-8 --parallel --max-workers=4 jar returned exit code 1
in a recent pbuilder chroot.
I would love to test igv, but it seems it does not build reliably. :-(
Kind regards
Andreas.
[1] https://salsa.debian.org/med-team/igv/commit/eaa95f1c5d56003c91984f1e2036bbf8bae7fec0