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opencb / biodata

Java library that models biological entities and their equivalents in different file formats typically used in bioinformatics
Apache License 2.0
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fix Pair issue (again?) #196

Closed julie-sullivan closed 3 years ago

julie-sullivan commented 3 years ago

I am having compilation issues. Maybe I have a cached library? I can try to delete all my local JARs?

I compiled these locally:

biodata-hotfix-1.5.x which needs commons - hotfix-3.7.x

Error 1:

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.6.0:compile (default-compile) on project biodata-models: Compilation failure: Compilation failure: 
[ERROR] /home/julie/git/biodata/biodata-models/src/main/java/org/opencb/biodata/models/variant/stats/VariantSampleStats.java:[3,19] package javafx.util does not exist
[ERROR] /home/julie/git/biodata/biodata-models/src/main/java/org/opencb/biodata/models/variant/stats/VariantSampleStats.java:[25,18] cannot find symbol
[ERROR]   symbol:   class Pair
[ERROR]   location: class org.opencb.biodata.models.variant.stats.VariantSampleStats
[ERROR] /home/julie/git/biodata/biodata-models/src/main/java/org/opencb/biodata/models/variant/stats/VariantSampleStats.java:[34,18] cannot find symbol
[ERROR]   symbol:   class Pair
[ERROR]   location: class org.opencb.biodata.models.variant.stats.VariantSampleStats
[ERROR] /home/julie/git/biodata/biodata-models/src/main/java/org/opencb/biodata/models/variant/stats/VariantSampleStats.java:[158,17] cannot find symbol
[ERROR]   symbol:   class Pair
[ERROR]   location: class org.opencb.biodata.models.variant.stats.VariantSampleStats
[ERROR] /home/julie/git/biodata/biodata-models/src/main/java/org/opencb/biodata/models/variant/stats/VariantSampleStats.java:[162,56] cannot find symbol
[ERROR]   symbol:   class Pair
[ERROR]   location: class org.opencb.biodata.models.variant.stats.VariantSampleStats
[ERROR] /home/julie/git/biodata/biodata-models/src/main/java/org/opencb/biodata/models/variant/stats/VariantSampleStats.java:[167,17] cannot find symbol
[ERROR]   symbol:   class Pair
[ERROR]   location: class org.opencb.biodata.models.variant.stats.VariantSampleStats
[ERROR] /home/julie/git/biodata/biodata-models/src/main/java/org/opencb/biodata/models/variant/stats/VariantSampleStats.java:[171,61] cannot find symbol
[ERROR]   symbol:   class Pair
[ERROR]   location: class org.opencb.biodata.models.variant.stats.VariantSampleStats
[ERROR] -> [Help 1]

Error 2:

# VariantStatsTsvExporterTest.java 
nextInt(int, int)' in 'org.apache.commons.lang3.RandomUtils' cannot be applied to '()'

Tests still don't pass though because I get this error:

Error 3:
# VariantStatsTsvExporterTest.java 
java.lang.NoClassDefFoundError: org/apache/logging/log4j/util/StackLocatorUtil
imedina commented 3 years ago

Looks good to me, thanks!