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drivenbyentropy / aptasuite

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.
https://drivenbyentropy.github.io/
GNU General Public License v3.0
24 stars 11 forks source link

Aptasuite/aptatrace isn't working well on mac #35

Closed barkait closed 6 years ago

barkait commented 6 years ago

hey, now when i used the CLI it works well but i can't enter the aptatrace tab on the gui, it give me the following errors:

terminal output: 

> java -jar aptasuite-0.6.3.jar 
objc[52022]: Class FIFinderSyncExtensionHost is implemented in both /System/Library/PrivateFrameworks/FinderKit.framework/Versions/A/FinderKit (0x7fff96e94b68) and /System/Library/PrivateFrameworks/FileProvider.framework/OverrideBundles/FinderSyncCollaborationFileProviderOverride.bundle/Contents/MacOS/FinderSyncCollaborationFileProviderOverride (0x13f740cd8). One of the two will be used. Which one is undefined.
Reading configuration from file.
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/Users/username/OneDrive/my_projects/Aptamers/aptasuite-0.6.3/lib/ch.qos.logback.logback-classic-1.1.3.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/Users/username/OneDrive/my_projects/Aptamers/aptasuite-0.6.3/lib/org.slf4j.slf4j-simple-1.7.12.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [ch.qos.logback.classic.util.ContextSelectorStaticBinder]
21:19:49.351 [JavaFX Application Thread] DEBUG o.a.c.b.converters.BooleanConverter - Setting default value: false
21:19:49.355 [JavaFX Application Thread] DEBUG o.a.c.b.converters.BooleanConverter - Converting 'Boolean' value 'false' to type 'Boolean'
21:19:49.355 [JavaFX Application Thread] DEBUG o.a.c.b.converters.BooleanConverter -     No conversion required, value is already a Boolean
21:19:49.359 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ByteConverter - Setting default value: 0
21:19:49.359 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ByteConverter - Converting 'Integer' value '0' to type 'Byte'
21:19:49.359 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ByteConverter -     Converted to Byte value '0'
21:19:49.360 [JavaFX Application Thread] DEBUG o.a.c.b.c.CharacterConverter - Setting default value:  
21:19:49.360 [JavaFX Application Thread] DEBUG o.a.c.b.c.CharacterConverter - Converting 'Character' value ' ' to type 'Character'
21:19:49.360 [JavaFX Application Thread] DEBUG o.a.c.b.c.CharacterConverter -     No conversion required, value is already a Character
21:19:49.361 [JavaFX Application Thread] DEBUG o.a.c.b.converters.DoubleConverter - Setting default value: 0
21:19:49.361 [JavaFX Application Thread] DEBUG o.a.c.b.converters.DoubleConverter - Converting 'Integer' value '0' to type 'Double'
21:19:49.361 [JavaFX Application Thread] DEBUG o.a.c.b.converters.DoubleConverter -     Converted to Double value '0.0'
21:19:49.362 [JavaFX Application Thread] DEBUG o.a.c.b.converters.FloatConverter - Setting default value: 0
21:19:49.362 [JavaFX Application Thread] DEBUG o.a.c.b.converters.FloatConverter - Converting 'Integer' value '0' to type 'Float'
21:19:49.362 [JavaFX Application Thread] DEBUG o.a.c.b.converters.FloatConverter -     Converted to Float value '0.0'
21:19:49.362 [JavaFX Application Thread] DEBUG o.a.c.b.converters.IntegerConverter - Setting default value: 0
21:19:49.362 [JavaFX Application Thread] DEBUG o.a.c.b.converters.IntegerConverter - Converting 'Integer' value '0' to type 'Integer'
21:19:49.362 [JavaFX Application Thread] DEBUG o.a.c.b.converters.IntegerConverter -     No conversion required, value is already a Integer
21:19:49.363 [JavaFX Application Thread] DEBUG o.a.c.b.converters.LongConverter - Setting default value: 0
21:19:49.363 [JavaFX Application Thread] DEBUG o.a.c.b.converters.LongConverter - Converting 'Integer' value '0' to type 'Long'
21:19:49.363 [JavaFX Application Thread] DEBUG o.a.c.b.converters.LongConverter -     Converted to Long value '0'
21:19:49.363 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ShortConverter - Setting default value: 0
21:19:49.364 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ShortConverter - Converting 'Integer' value '0' to type 'Short'
21:19:49.364 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ShortConverter -     Converted to Short value '0'
21:19:49.366 [JavaFX Application Thread] DEBUG o.a.c.b.c.BigDecimalConverter - Setting default value: 0.0
21:19:49.366 [JavaFX Application Thread] DEBUG o.a.c.b.c.BigDecimalConverter - Converting 'BigDecimal' value '0.0' to type 'BigDecimal'
21:19:49.366 [JavaFX Application Thread] DEBUG o.a.c.b.c.BigDecimalConverter -     No conversion required, value is already a BigDecimal
21:19:49.367 [JavaFX Application Thread] DEBUG o.a.c.b.c.BigIntegerConverter - Setting default value: 0
21:19:49.367 [JavaFX Application Thread] DEBUG o.a.c.b.c.BigIntegerConverter - Converting 'BigInteger' value '0' to type 'BigInteger'
21:19:49.367 [JavaFX Application Thread] DEBUG o.a.c.b.c.BigIntegerConverter -     No conversion required, value is already a BigInteger
21:19:49.367 [JavaFX Application Thread] DEBUG o.a.c.b.converters.BooleanConverter - Setting default value: false
21:19:49.367 [JavaFX Application Thread] DEBUG o.a.c.b.converters.BooleanConverter - Converting 'Boolean' value 'false' to type 'Boolean'
21:19:49.367 [JavaFX Application Thread] DEBUG o.a.c.b.converters.BooleanConverter -     No conversion required, value is already a Boolean
21:19:49.367 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ByteConverter - Setting default value: 0
21:19:49.367 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ByteConverter - Converting 'Integer' value '0' to type 'Byte'
21:19:49.367 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ByteConverter -     Converted to Byte value '0'
21:19:49.367 [JavaFX Application Thread] DEBUG o.a.c.b.c.CharacterConverter - Setting default value:  
21:19:49.367 [JavaFX Application Thread] DEBUG o.a.c.b.c.CharacterConverter - Converting 'Character' value ' ' to type 'Character'
21:19:49.368 [JavaFX Application Thread] DEBUG o.a.c.b.c.CharacterConverter -     No conversion required, value is already a Character
21:19:49.368 [JavaFX Application Thread] DEBUG o.a.c.b.converters.DoubleConverter - Setting default value: 0
21:19:49.368 [JavaFX Application Thread] DEBUG o.a.c.b.converters.DoubleConverter - Converting 'Integer' value '0' to type 'Double'
21:19:49.368 [JavaFX Application Thread] DEBUG o.a.c.b.converters.DoubleConverter -     Converted to Double value '0.0'
21:19:49.368 [JavaFX Application Thread] DEBUG o.a.c.b.converters.FloatConverter - Setting default value: 0
21:19:49.368 [JavaFX Application Thread] DEBUG o.a.c.b.converters.FloatConverter - Converting 'Integer' value '0' to type 'Float'
21:19:49.368 [JavaFX Application Thread] DEBUG o.a.c.b.converters.FloatConverter -     Converted to Float value '0.0'
21:19:49.368 [JavaFX Application Thread] DEBUG o.a.c.b.converters.IntegerConverter - Setting default value: 0
21:19:49.368 [JavaFX Application Thread] DEBUG o.a.c.b.converters.IntegerConverter - Converting 'Integer' value '0' to type 'Integer'
21:19:49.368 [JavaFX Application Thread] DEBUG o.a.c.b.converters.IntegerConverter -     No conversion required, value is already a Integer
21:19:49.368 [JavaFX Application Thread] DEBUG o.a.c.b.converters.LongConverter - Setting default value: 0
21:19:49.369 [JavaFX Application Thread] DEBUG o.a.c.b.converters.LongConverter - Converting 'Integer' value '0' to type 'Long'
21:19:49.369 [JavaFX Application Thread] DEBUG o.a.c.b.converters.LongConverter -     Converted to Long value '0'
21:19:49.369 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ShortConverter - Setting default value: 0
21:19:49.369 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ShortConverter - Converting 'Integer' value '0' to type 'Short'
21:19:49.369 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ShortConverter -     Converted to Short value '0'
21:19:49.369 [JavaFX Application Thread] DEBUG o.a.c.b.converters.StringConverter - Setting default value: 
21:19:49.370 [JavaFX Application Thread] DEBUG o.a.c.b.converters.StringConverter - Converting 'String' value '' to type 'String'
21:19:49.377 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Z@2a59ca3b
21:19:49.378 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'boolean[]' value '[Z@2a59ca3b' to type 'boolean[]'
21:19:49.378 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a boolean[]
21:19:49.378 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [B@3da9f580
21:19:49.378 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'byte[]' value '[B@3da9f580' to type 'byte[]'
21:19:49.378 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a byte[]
21:19:49.378 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [C@35827cd
21:19:49.378 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'char[]' value '[C@35827cd' to type 'char[]'
21:19:49.378 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a char[]
21:19:49.378 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [D@510cb4ba
21:19:49.378 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'double[]' value '[D@510cb4ba' to type 'double[]'
21:19:49.378 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a double[]
21:19:49.378 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [F@615f7313
21:19:49.378 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'float[]' value '[F@615f7313' to type 'float[]'
21:19:49.379 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a float[]
21:19:49.379 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [I@655349b0
21:19:49.379 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'int[]' value '[I@655349b0' to type 'int[]'
21:19:49.379 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a int[]
21:19:49.379 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [J@1ca677da
21:19:49.379 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'long[]' value '[J@1ca677da' to type 'long[]'
21:19:49.379 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a long[]
21:19:49.379 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [S@2362d288
21:19:49.379 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'short[]' value '[S@2362d288' to type 'short[]'
21:19:49.379 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a short[]
21:19:49.379 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.math.BigDecimal;@7334b560
21:19:49.379 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'BigDecimal[]' value '[Ljava.math.BigDecimal;@7334b560' to type 'BigDecimal[]'
21:19:49.379 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a BigDecimal[]
21:19:49.380 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.math.BigInteger;@1a959ca8
21:19:49.380 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'BigInteger[]' value '[Ljava.math.BigInteger;@1a959ca8' to type 'BigInteger[]'
21:19:49.380 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a BigInteger[]
21:19:49.380 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Boolean;@8975880
21:19:49.380 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Boolean[]' value '[Ljava.lang.Boolean;@8975880' to type 'Boolean[]'
21:19:49.380 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Boolean[]
21:19:49.380 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Byte;@26f5e685
21:19:49.380 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Byte[]' value '[Ljava.lang.Byte;@26f5e685' to type 'Byte[]'
21:19:49.380 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Byte[]
21:19:49.380 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Character;@39ab637d
21:19:49.380 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Character[]' value '[Ljava.lang.Character;@39ab637d' to type 'Character[]'
21:19:49.380 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Character[]
21:19:49.381 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Double;@3a9df9ee
21:19:49.381 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Double[]' value '[Ljava.lang.Double;@3a9df9ee' to type 'Double[]'
21:19:49.381 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Double[]
21:19:49.381 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Float;@93c4d6
21:19:49.381 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Float[]' value '[Ljava.lang.Float;@93c4d6' to type 'Float[]'
21:19:49.381 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Float[]
21:19:49.381 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Integer;@495b57ff
21:19:49.381 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Integer[]' value '[Ljava.lang.Integer;@495b57ff' to type 'Integer[]'
21:19:49.381 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Integer[]
21:19:49.381 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Long;@3a4772a0
21:19:49.381 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Long[]' value '[Ljava.lang.Long;@3a4772a0' to type 'Long[]'
21:19:49.381 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Long[]
21:19:49.381 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Short;@429bc6fc
21:19:49.381 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Short[]' value '[Ljava.lang.Short;@429bc6fc' to type 'Short[]'
21:19:49.382 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Short[]
21:19:49.382 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.String;@10fd9092
21:19:49.382 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'String[]' value '[Ljava.lang.String;@10fd9092' to type 'String[]'
21:19:49.382 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a String[]
21:19:49.382 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Class;@11ae225f
21:19:49.382 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Class[]' value '[Ljava.lang.Class;@11ae225f' to type 'Class[]'
21:19:49.382 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Class[]
21:19:49.382 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.util.Date;@d1eaab0
21:19:49.382 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Date[]' value '[Ljava.util.Date;@d1eaab0' to type 'Date[]'
21:19:49.383 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Date[]
21:19:49.383 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.util.Calendar;@446d6b1e
21:19:49.383 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Calendar[]' value '[Ljava.util.Calendar;@446d6b1e' to type 'Calendar[]'
21:19:49.383 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Calendar[]
21:19:49.383 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.io.File;@5c02601a
21:19:49.383 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.io.File[]' value '[Ljava.io.File;@5c02601a' to type 'java.io.File[]'
21:19:49.383 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a java.io.File[]
21:19:49.384 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.sql.Date;@b249804
21:19:49.384 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.sql.Date[]' value '[Ljava.sql.Date;@b249804' to type 'java.sql.Date[]'
21:19:49.384 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a java.sql.Date[]
21:19:49.384 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.sql.Time;@685c939b
21:19:49.384 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.sql.Time[]' value '[Ljava.sql.Time;@685c939b' to type 'java.sql.Time[]'
21:19:49.384 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a java.sql.Time[]
21:19:49.384 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.sql.Timestamp;@126cf91c
21:19:49.384 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.sql.Timestamp[]' value '[Ljava.sql.Timestamp;@126cf91c' to type 'java.sql.Timestamp[]'
21:19:49.384 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a java.sql.Timestamp[]
21:19:49.384 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.net.URL;@30b1e570
21:19:49.384 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.net.URL[]' value '[Ljava.net.URL;@30b1e570' to type 'java.net.URL[]'
21:19:49.385 [JavaFX Application Thread] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a java.net.URL[]
21:19:49.439 [JavaFX Application Thread] INFO  o.a.c.b.FluentPropertyBeanIntrospector - Error when creating PropertyDescriptor for public final void org.apache.commons.configuration2.AbstractConfiguration.setProperty(java.lang.String,java.lang.Object)! Ignoring this property.
21:19:49.448 [JavaFX Application Thread] DEBUG o.a.c.b.FluentPropertyBeanIntrospector - Exception is:
java.beans.IntrospectionException: bad write method arg count: public final void org.apache.commons.configuration2.AbstractConfiguration.setProperty(java.lang.String,java.lang.Object)
    at java.desktop/java.beans.PropertyDescriptor.findPropertyType(PropertyDescriptor.java:696) ~[na:na]
    at java.desktop/java.beans.PropertyDescriptor.setWriteMethod(PropertyDescriptor.java:356) ~[na:na]
    at java.desktop/java.beans.PropertyDescriptor.<init>(PropertyDescriptor.java:142) ~[na:na]
    at org.apache.commons.beanutils.FluentPropertyBeanIntrospector.createFluentPropertyDescritor(FluentPropertyBeanIntrospector.java:178) ~[commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
    at org.apache.commons.beanutils.FluentPropertyBeanIntrospector.introspect(FluentPropertyBeanIntrospector.java:141) ~[commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
    at org.apache.commons.beanutils.PropertyUtilsBean.fetchIntrospectionData(PropertyUtilsBean.java:2245) [commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
    at org.apache.commons.beanutils.PropertyUtilsBean.getIntrospectionData(PropertyUtilsBean.java:2226) [commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
    at org.apache.commons.beanutils.PropertyUtilsBean.getPropertyDescriptor(PropertyUtilsBean.java:954) [commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
    at org.apache.commons.beanutils.PropertyUtilsBean.isWriteable(PropertyUtilsBean.java:1478) [commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
    at org.apache.commons.configuration2.beanutils.BeanHelper.isPropertyWriteable(BeanHelper.java:521) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
    at org.apache.commons.configuration2.beanutils.BeanHelper.initProperty(BeanHelper.java:357) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
    at org.apache.commons.configuration2.beanutils.BeanHelper.initBeanProperties(BeanHelper.java:273) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
    at org.apache.commons.configuration2.beanutils.BeanHelper.initBean(BeanHelper.java:192) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
    at org.apache.commons.configuration2.beanutils.BeanHelper$BeanCreationContextImpl.initBean(BeanHelper.java:669) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
    at org.apache.commons.configuration2.beanutils.DefaultBeanFactory.initBeanInstance(DefaultBeanFactory.java:162) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
    at org.apache.commons.configuration2.beanutils.DefaultBeanFactory.createBean(DefaultBeanFactory.java:116) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
    at org.apache.commons.configuration2.beanutils.BeanHelper.createBean(BeanHelper.java:459) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
    at org.apache.commons.configuration2.beanutils.BeanHelper.createBean(BeanHelper.java:479) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
    at org.apache.commons.configuration2.beanutils.BeanHelper.createBean(BeanHelper.java:492) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
    at org.apache.commons.configuration2.builder.BasicConfigurationBuilder.createResultInstance(BasicConfigurationBuilder.java:447) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
    at org.apache.commons.configuration2.builder.BasicConfigurationBuilder.createResult(BasicConfigurationBuilder.java:417) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
    at org.apache.commons.configuration2.builder.BasicConfigurationBuilder.getConfiguration(BasicConfigurationBuilder.java:285) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
    at utilities.Configuration.setConfiguration(Configuration.java:209) [aptasuite-0.6.3.jar:na]
    at gui.core.RootLayoutController.fileOpenExperimentButtonAction(RootLayoutController.java:391) [aptasuite-0.6.3.jar:na]
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:na]
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:na]
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:na]
    at java.base/java.lang.reflect.Method.invoke(Method.java:564) ~[na:na]
    at com.sun.javafx.reflect.Trampoline.invoke(MethodUtil.java:76) [na:na]
    at jdk.internal.reflect.GeneratedMethodAccessor2.invoke(Unknown Source) ~[na:na]
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:na]
    at java.base/java.lang.reflect.Method.invoke(Method.java:564) ~[na:na]
    at javafx.base/com.sun.javafx.reflect.MethodUtil.invoke(MethodUtil.java:275) [javafx.base:na]
    at javafx.fxml/com.sun.javafx.fxml.MethodHelper.invoke(MethodHelper.java:83) [javafx.fxml:na]
    at javafx.fxml/javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1782) [javafx.fxml:na]
    at javafx.fxml/javafx.fxml.FXMLLoader$ControllerMethodEventHandler.handle(FXMLLoader.java:1670) [javafx.fxml:na]
    at javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) [javafx.base:na]
    at javafx.base/javafx.event.Event.fireEvent(Event.java:198) [javafx.base:na]
    at javafx.controls/javafx.scene.control.MenuItem.fire(MenuItem.java:465) [javafx.controls:na]
    at javafx.controls/com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.doSelect(ContextMenuContent.java:1380) [javafx.controls:na]
    at javafx.controls/com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.lambda$createChildren$12(ContextMenuContent.java:1333) [javafx.controls:na]
    at javafx.base/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218) ~[javafx.base:na]
    at javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) ~[javafx.base:na]
    at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) [javafx.base:na]
    at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) [javafx.base:na]
    at javafx.base/javafx.event.Event.fireEvent(Event.java:198) [javafx.base:na]
    at javafx.graphics/javafx.scene.Scene$MouseHandler.process(Scene.java:3876) ~[javafx.graphics:na]
    at javafx.graphics/javafx.scene.Scene$MouseHandler.access$1300(Scene.java:3604) ~[javafx.graphics:na]
    at javafx.graphics/javafx.scene.Scene.processMouseEvent(Scene.java:1874) ~[javafx.graphics:na]
    at javafx.graphics/javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2613) ~[javafx.graphics:na]
    at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:397) ~[javafx.graphics:na]
    at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:295) ~[javafx.graphics:na]
    at java.base/java.security.AccessController.doPrivileged(Native Method) ~[na:na]
    at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:434) ~[javafx.graphics:na]
    at javafx.graphics/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:389) ~[javafx.graphics:na]
    at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:433) ~[javafx.graphics:na]
    at javafx.graphics/com.sun.glass.ui.View.handleMouseEvent(View.java:556) ~[javafx.graphics:na]
    at javafx.graphics/com.sun.glass.ui.View.notifyMouse(View.java:942) ~[javafx.graphics:na]
    at javafx.graphics/com.sun.glass.ui.mac.MacView.notifyMouse(MacView.java:127) ~[javafx.graphics:na]
Instantiating MapDBAptamerPool
Searching for existing datasets in /Users/username/Desktop/2018-02-24_17-50-24_test/pooldata
Processing /Users/username/Desktop/2018-02-24_17-50-24_test/pooldata/data0000.mapdb
Found and loaded a total of 18301 aptamers from disk.
Processing selection cycle Round0
Processing selection cycle Round1
Loading took 2658 milliseconds
Initializing GUI elements
Initializing Motif Analysis Content
Exception in thread "JavaFX Application Thread" java.lang.NoSuchMethodError: com.sun.javafx.tk.FontMetrics.computeStringWidth(Ljava/lang/String;)F
    at gui.core.motifs.MotifAnalysisRootController.generateColumn(MotifAnalysisRootController.java:812)
    at gui.core.motifs.MotifAnalysisRootController.createTable(MotifAnalysisRootController.java:650)
    at gui.core.motifs.MotifAnalysisRootController.initializeControlBars(MotifAnalysisRootController.java:382)
    at gui.core.motifs.MotifAnalysisRootController.initializeContent(MotifAnalysisRootController.java:257)
    at gui.core.RootLayoutController$1.changed(RootLayoutController.java:184)
    at gui.core.RootLayoutController$1.changed(RootLayoutController.java:176)
    at javafx.base/com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:360)
    at javafx.base/com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80)
    at javafx.base/javafx.beans.property.ReadOnlyObjectPropertyBase.fireValueChangedEvent(ReadOnlyObjectPropertyBase.java:74)
    at javafx.base/javafx.beans.property.ReadOnlyObjectWrapper.fireValueChangedEvent(ReadOnlyObjectWrapper.java:102)
    at javafx.base/javafx.beans.property.ObjectPropertyBase.markInvalid(ObjectPropertyBase.java:113)
    at javafx.base/javafx.beans.property.ObjectPropertyBase.set(ObjectPropertyBase.java:147)
    at javafx.controls/javafx.scene.control.SelectionModel.setSelectedItem(SelectionModel.java:105)
    at javafx.controls/javafx.scene.control.TabPane$TabPaneSelectionModel.select(TabPane.java:733)
    at javafx.controls/javafx.scene.control.TabPane$TabPaneSelectionModel.select(TabPane.java:751)
    at javafx.controls/javafx.scene.control.TabPane$TabPaneSelectionModel.select(TabPane.java:672)
    at javafx.controls/com.sun.javafx.scene.control.behavior.TabPaneBehavior.selectTab(TabPaneBehavior.java:82)
    at javafx.controls/javafx.scene.control.skin.TabPaneSkin$TabHeaderSkin$5.handle(TabPaneSkin.java:1476)
    at javafx.controls/javafx.scene.control.skin.TabPaneSkin$TabHeaderSkin$5.handle(TabPaneSkin.java:1462)
    at javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at javafx.base/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
    at javafx.base/javafx.event.Event.fireEvent(Event.java:198)
    at javafx.graphics/javafx.scene.Scene$MouseHandler.process(Scene.java:3876)
    at javafx.graphics/javafx.scene.Scene$MouseHandler.access$1300(Scene.java:3604)
    at javafx.graphics/javafx.scene.Scene.processMouseEvent(Scene.java:1874)
    at javafx.graphics/javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2613)
    at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:397)
    at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:295)
    at java.base/java.security.AccessController.doPrivileged(Native Method)
    at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:434)
    at javafx.graphics/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:389)
    at javafx.graphics/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:433)
    at javafx.graphics/com.sun.glass.ui.View.handleMouseEvent(View.java:556)
    at javafx.graphics/com.sun.glass.ui.View.notifyMouse(View.java:942)
    at javafx.graphics/com.sun.glass.ui.mac.MacView.notifyMouse(MacView.java:127)
Exiting

config file:

> Experiment.name = test
Experiment.description = test
Experiment.primer5 = GGGAGGACGATGCGG
Experiment.primer3 = CAGACGACTCGCCCGA
Experiment.randomizedRegionSize = 40
AptaplexParser.isPerFile = true
AptaplexParser.reader = FastqReader
SelectionCycle.name = Round0
SelectionCycle.name = Round1
SelectionCycle.round = 0
SelectionCycle.round = 1
SelectionCycle.isControlSelection = false
SelectionCycle.isControlSelection = false
SelectionCycle.isCounterSelection = false
SelectionCycle.isCounterSelection = false
AptaplexParser.forwardFiles = /Users/username/Desktop/2018-02-24_17-50-24_test/SRR3510044_SHORT.fastq
AptaplexParser.forwardFiles = /Users/username/Desktop/2018-02-24_17-50-24_test/SRR3510053_SHORT.fastq
Experiment.projectPath = /Users/username/Desktop/2018-02-24_17-50-24_test
Performance.maxNumberOfCores = 4

log file (i cant add it so i paste it):

[9:19:49 | CONFIG | Thread-4]: aptasuite.Aptasuite
System Information:
Java Version: 9.0.1
JavaFX Version: null
OS Name: Mac OS X
OS Version: 10.13.3
OS Architecture: x86_64
CPU cores: 4
System Memory: 134217728 Mb

[9:19:49 | INFO | Thread-4]: utilities.Configuration
Reading configuration from file. 

[9:19:49 | INFO | Thread-4]: lib.aptamer.datastructures.MapDBAptamerPool
Instantiating MapDBAptamerPool 

[9:19:49 | INFO | Thread-4]: lib.aptamer.datastructures.MapDBAptamerPool
Searching for existing datasets in /Users/username/Desktop/2018-02-24_17-50-24_test/pooldata 

[9:19:49 | INFO | Thread-4]: lib.aptamer.datastructures.MapDBAptamerPool
Processing /Users/username/Desktop/2018-02-24_17-50-24_test/pooldata/data0000.mapdb 

[9:19:51 | CONFIG | Thread-4]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from /Users/username/Desktop/2018-02-24_17-50-24_test/pooldata/inverse_data0000.mapdb 

[9:19:51 | CONFIG | Thread-4]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from /Users/username/Desktop/2018-02-24_17-50-24_test/pooldata/bounds_data0000.mapdb 

[9:19:51 | CONFIG | Thread-4]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 18301
Total number of aptamers: 18301
Processed in 1.379 seconds. 

[9:19:51 | INFO | Thread-4]: lib.aptamer.datastructures.MapDBAptamerPool
Found and loaded a total of 18301 aptamers from disk. 

[9:19:51 | CONFIG | Thread-4]: lib.aptamer.datastructures.MapDBAptamerPool
AptamerPool instantiation took 1.412 seconds 

[9:19:51 | INFO | Thread-4]: lib.aptamer.datastructures.MapDBSelectionCycle
Processing selection cycle Round0 

[9:19:51 | CONFIG | Thread-4]: lib.aptamer.datastructures.MapDBSelectionCycle
Reading from file '/Users/username/Desktop/2018-02-24_17-50-24_test/cycledata/0_Round0.mapdb' for selection cycle Round0. 

[9:19:52 | INFO | Thread-4]: lib.aptamer.datastructures.MapDBSelectionCycle
Processing selection cycle Round1 

[9:19:52 | CONFIG | Thread-4]: lib.aptamer.datastructures.MapDBSelectionCycle
Reading from file '/Users/username/Desktop/2018-02-24_17-50-24_test/cycledata/1_Round1.mapdb' for selection cycle Round1. 

[9:19:52 | CONFIG | Thread-4]: lib.aptamer.datastructures.Metadata
Reading metadata file from '/Users/username/Desktop/2018-02-24_17-50-24_test/metadata.mapdb 

[9:19:52 | INFO | Thread-4]: lib.aptamer.datastructures.Experiment
Loading took 2658 milliseconds 

[9:19:52 | INFO | JavaFX Application Thread]: gui.core.RootLayoutController$3
Initializing GUI elements 

[9:19:52 | CONFIG | JavaFX Application Thread]: utilities.Configuration
Written Configuration file to /Users/username/Desktop/2018-02-24_17-50-24_test/configuration.aptasuite 

[9:20:01 | INFO | JavaFX Application Thread]: gui.core.motifs.MotifAnalysisRootController
Initializing Motif Analysis Content

thanks!

drivenbyentropy commented 6 years ago

Thank you for reporting this.

It seems to me that all these issues are related to using Java 9 as opposed to Java 8 which was the version I targeted when developing AptaSuite.

I will look into this as soon as I get my development environment to use Java 9.

Meanwhile, the only thing I can recommend, is to use Java 8.

Sorry for the inconvenience and thanks again.

drivenbyentropy commented 6 years ago

The lastest commit should have fixed this. Please let me know if you still encounter issues with related with this ticket for versions v0.7.2 or higher.

k-fhung commented 2 years ago

Hi, I cannot install aptasuite with the macOS Monterey. Is it possible to provide a detail instruction for this? Thank you