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PRIDE-Toolsuite / PRIDEParametersExtractor

The PRIDEParametersExtractor retrieve the search parameters from Complete Submissions in PRIDE.
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How to build? #1

Open alephreish opened 6 years ago

alephreish commented 6 years ago

There are no README or INSTALL in the repository, neither are there any releases, or maven repositories.

mvn compile fails with 'Could not find artifact com.compomics.pride-asa-pipeline:pride-asa-pipeline-core:jar:1.7.4.faster'. I couldn't find the 1.7.4.faster version of pride-asa-pipeline, but compilation against the latest version from github (1.7.3-SNAPSHOT) fails with:

mvn compile output [INFO] Scanning for projects... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building pride-parameters 0.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots/psidev/psi/tools/master-pom/4-SNAPSHOT/maven-metadata.xml Downloading: http://www.ebi.ac.uk/intact/maven/nexus/content/groups/public/psidev/psi/tools/master-pom/4-SNAPSHOT/maven-metadata.xml [WARNING] Could not transfer metadata psidev.psi.tools:master-pom:4-SNAPSHOT/maven-metadata.xml from/to nexus-ebi-repo-snapshots (http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots): Failed to transfer file: http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots/psidev/psi/tools/master-pom/4-SNAPSHOT/maven-metadata.xml. Return code is: 500 , ReasonPhrase:Server Error. [WARNING] Could not transfer metadata psidev.psi.tools:master-pom:4-SNAPSHOT/maven-metadata.xml from/to intact.nexus (http://www.ebi.ac.uk/intact/maven/nexus/content/groups/public/): Failed to transfer file: http://www.ebi.ac.uk/intact/maven/nexus/content/groups/public/psidev/psi/tools/master-pom/4-SNAPSHOT/maven-metadata.xml. Return code is: 500 , ReasonPhrase:Server Error. [WARNING] The POM for batik:pdf-transcoder:jar:1.0 is missing, no dependency information available [WARNING] The POM for umontreal.iro.lecuyer.gof:ssj:jar:2.5.0 is missing, no dependency information available [WARNING] The POM for net.jimmc:jshortcut:jar:0.4-oberzalek is missing, no dependency information available [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ pride-parameters --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] Copying 12 resources [INFO] [INFO] --- maven-resources-plugin:2.6:copy-resources (copy-package-resources) @ pride-parameters --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 4 resources [INFO] [INFO] --- maven-resources-plugin:2.6:copy-resources (copy-package-license) @ pride-parameters --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.2:compile (default-compile) @ pride-parameters --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 12 source files to /my/path/PRIDEParametersExtractor/target/classes [INFO] ------------------------------------------------------------- [ERROR] COMPILATION ERROR : [INFO] ------------------------------------------------------------- [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/PRIDERefinery.java:[3,60] cannot find symbol symbol: class IParametersRefinery location: package com.compomics.pride_asa_pipeline.core.data.extractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/PRIDERefinery.java:[25,39] cannot find symbol symbol: class IParametersRefinery [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[3,46] cannot find symbol symbol: class ParameterExtractionException location: package com.compomics.pride_asa_pipeline.model [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[4,64] package com.compomics.pride_asa_pipeline.model.modification.impl does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[7,42] package uk.ac.ebi.pride.utilities.pridemod does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[8,48] package uk.ac.ebi.pride.utilities.pridemod.model does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[9,48] package uk.ac.ebi.pride.utilities.pridemod.model does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[35,18] cannot find symbol symbol: class ModReader location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[38,18] cannot find symbol symbol: class UtilitiesPTMAdapter location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[40,82] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[61,90] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[129,101] package uk.ac.ebi.pride.utilities.pridemod.model does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[3,46] cannot find symbol symbol: class MGFExtractionException location: package com.compomics.pride_asa_pipeline.model [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[4,46] cannot find symbol symbol: class ParameterExtractionException location: package com.compomics.pride_asa_pipeline.model [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[13,38] cannot find symbol symbol: class DigestionPreferences location: package com.compomics.util.preferences [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/PrideParameterExtractor.java:[3,46] cannot find symbol symbol: class MGFExtractionException location: package com.compomics.pride_asa_pipeline.model [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/PrideParameterExtractor.java:[4,46] cannot find symbol symbol: class ParameterExtractionException location: package com.compomics.pride_asa_pipeline.model [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[51,37] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[51,105] cannot find symbol symbol: class MGFExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[63,65] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/PrideParameterExtractor.java:[21,37] cannot find symbol symbol: class ParameterExtractionException location: interface com.compomics.pridesearchparameterextractor.extraction.PrideParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/PrideParameterExtractor.java:[21,105] cannot find symbol symbol: class MGFExtractionException location: interface com.compomics.pridesearchparameterextractor.extraction.PrideParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[3,60] cannot find symbol symbol: class FileParameterExtractor location: package com.compomics.pride_asa_pipeline.core.data.extractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[4,60] cannot find symbol symbol: class IParametersRefinery location: package com.compomics.pride_asa_pipeline.core.data.extractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[5,46] cannot find symbol symbol: class ParameterExtractionException location: package com.compomics.pride_asa_pipeline.model [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[49,13] cannot find symbol symbol: class IParametersRefinery location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[62,91] cannot find symbol symbol: class IParametersRefinery location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[62,128] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[77,126] cannot find symbol symbol: class IParametersRefinery location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[94,74] cannot find symbol symbol: class IParametersRefinery location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[94,111] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[3,60] cannot find symbol symbol: class FileParameterExtractor location: package com.compomics.pride_asa_pipeline.core.data.extractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[4,60] cannot find symbol symbol: class IParametersRefinery location: package com.compomics.pride_asa_pipeline.core.data.extractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[5,46] cannot find symbol symbol: class MGFExtractionException location: package com.compomics.pride_asa_pipeline.model [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[6,46] cannot find symbol symbol: class ParameterExtractionException location: package com.compomics.pride_asa_pipeline.model [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[36,13] cannot find symbol symbol: class IParametersRefinery location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[65,114] cannot find symbol symbol: class IParametersRefinery location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[65,151] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[82,97] cannot find symbol symbol: class IParametersRefinery location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[82,134] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[89,149] cannot find symbol symbol: class IParametersRefinery location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[107,37] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[107,105] cannot find symbol symbol: class MGFExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/PRIDERefinery.java:[29,5] method does not override or implement a method from a supertype [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[35,40] cannot find symbol symbol: variable ModReader location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[38,52] cannot find symbol symbol: class UtilitiesPTMAdapter location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[55,31] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[74,58] package uk.ac.ebi.pride.utilities.pridemod.model does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[76,27] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[79,64] cannot find symbol symbol: class UniModPTM location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[83,27] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[86,66] package Specificity.Position does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[87,100] package Specificity.Position does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[94,72] package Specificity.Position does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[95,100] package Specificity.Position does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[110,23] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[123,44] package Specificity.Position does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[125,44] package Specificity.Position does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[143,18] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[58,22] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[75,23] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[82,23] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[87,23] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[93,23] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[108,23] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[114,23] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[121,23] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[125,23] cannot find symbol symbol: class ParameterExtractionException location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[127,9] cannot find symbol symbol: class DigestionPreferences location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[127,55] cannot find symbol symbol: class DigestionPreferences location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[130,69] package DigestionPreferences does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemEnzyme.java:[47,63] no suitable constructor found for Enzyme(java.lang.String) constructor com.compomics.util.experiment.biology.Enzyme.Enzyme(int,java.lang.String,java.lang.String,java.lang.String,java.lang.String,java.lang.String) is not applicable (actual and formal argument lists differ in length) constructor com.compomics.util.experiment.biology.Enzyme.Enzyme(int,java.lang.String,java.lang.String,java.lang.String,java.lang.String,java.lang.String,java.lang.Boolean,java.lang.Boolean) is not applicable (actual and formal argument lists differ in length) [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemEnzyme.java:[50,23] cannot find symbol symbol: method addAminoAcidBefore(java.lang.Character) location: variable enzyme of type com.compomics.util.experiment.biology.Enzyme [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemEnzyme.java:[53,23] cannot find symbol symbol: method addRestrictionAfter(java.lang.Character) location: variable enzyme of type com.compomics.util.experiment.biology.Enzyme [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemEnzyme.java:[54,15] cannot find symbol symbol: method setCvTerm(com.compomics.util.pride.CvTerm) location: variable enzyme of type com.compomics.util.experiment.biology.Enzyme [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[109,9] cannot find symbol symbol: class FileParameterExtractor location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[112,33] cannot find symbol symbol: class FileParameterExtractor location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[114,33] cannot find symbol symbol: class FileParameterExtractor location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[109,9] cannot find symbol symbol: class FileParameterExtractor location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[112,34] cannot find symbol symbol: class FileParameterExtractor location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[114,34] cannot find symbol symbol: class FileParameterExtractor location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [INFO] 81 errors [INFO] ------------------------------------------------------------- [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 4.040 s [INFO] Finished at: 2018-06-18T00:22:07+03:00 [INFO] Final Memory: 32M/244M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.2:compile (default-compile) on project pride-parameters: Compilation failure: Compilation failure: [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/PRIDERefinery.java:[3,60] cannot find symbol [ERROR] symbol: class IParametersRefinery [ERROR] location: package com.compomics.pride_asa_pipeline.core.data.extractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/PRIDERefinery.java:[25,39] cannot find symbol [ERROR] symbol: class IParametersRefinery [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[3,46] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: package com.compomics.pride_asa_pipeline.model [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[4,64] package com.compomics.pride_asa_pipeline.model.modification.impl does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[7,42] package uk.ac.ebi.pride.utilities.pridemod does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[8,48] package uk.ac.ebi.pride.utilities.pridemod.model does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[9,48] package uk.ac.ebi.pride.utilities.pridemod.model does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[35,18] cannot find symbol [ERROR] symbol: class ModReader [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[38,18] cannot find symbol [ERROR] symbol: class UtilitiesPTMAdapter [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[40,82] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[61,90] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[129,101] package uk.ac.ebi.pride.utilities.pridemod.model does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[3,46] cannot find symbol [ERROR] symbol: class MGFExtractionException [ERROR] location: package com.compomics.pride_asa_pipeline.model [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[4,46] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: package com.compomics.pride_asa_pipeline.model [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[13,38] cannot find symbol [ERROR] symbol: class DigestionPreferences [ERROR] location: package com.compomics.util.preferences [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/PrideParameterExtractor.java:[3,46] cannot find symbol [ERROR] symbol: class MGFExtractionException [ERROR] location: package com.compomics.pride_asa_pipeline.model [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/PrideParameterExtractor.java:[4,46] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: package com.compomics.pride_asa_pipeline.model [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[51,37] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[51,105] cannot find symbol [ERROR] symbol: class MGFExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[63,65] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/PrideParameterExtractor.java:[21,37] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: interface com.compomics.pridesearchparameterextractor.extraction.PrideParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/PrideParameterExtractor.java:[21,105] cannot find symbol [ERROR] symbol: class MGFExtractionException [ERROR] location: interface com.compomics.pridesearchparameterextractor.extraction.PrideParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[3,60] cannot find symbol [ERROR] symbol: class FileParameterExtractor [ERROR] location: package com.compomics.pride_asa_pipeline.core.data.extractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[4,60] cannot find symbol [ERROR] symbol: class IParametersRefinery [ERROR] location: package com.compomics.pride_asa_pipeline.core.data.extractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[5,46] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: package com.compomics.pride_asa_pipeline.model [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[49,13] cannot find symbol [ERROR] symbol: class IParametersRefinery [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[62,91] cannot find symbol [ERROR] symbol: class IParametersRefinery [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[62,128] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[77,126] cannot find symbol [ERROR] symbol: class IParametersRefinery [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[94,74] cannot find symbol [ERROR] symbol: class IParametersRefinery [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[94,111] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[3,60] cannot find symbol [ERROR] symbol: class FileParameterExtractor [ERROR] location: package com.compomics.pride_asa_pipeline.core.data.extractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[4,60] cannot find symbol [ERROR] symbol: class IParametersRefinery [ERROR] location: package com.compomics.pride_asa_pipeline.core.data.extractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[5,46] cannot find symbol [ERROR] symbol: class MGFExtractionException [ERROR] location: package com.compomics.pride_asa_pipeline.model [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[6,46] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: package com.compomics.pride_asa_pipeline.model [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[36,13] cannot find symbol [ERROR] symbol: class IParametersRefinery [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[65,114] cannot find symbol [ERROR] symbol: class IParametersRefinery [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[65,151] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[82,97] cannot find symbol [ERROR] symbol: class IParametersRefinery [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[82,134] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[89,149] cannot find symbol [ERROR] symbol: class IParametersRefinery [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[107,37] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[107,105] cannot find symbol [ERROR] symbol: class MGFExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/PRIDERefinery.java:[29,5] method does not override or implement a method from a supertype [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[35,40] cannot find symbol [ERROR] symbol: variable ModReader [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[38,52] cannot find symbol [ERROR] symbol: class UtilitiesPTMAdapter [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[55,31] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[74,58] package uk.ac.ebi.pride.utilities.pridemod.model does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[76,27] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[79,64] cannot find symbol [ERROR] symbol: class UniModPTM [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[83,27] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[86,66] package Specificity.Position does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[87,100] package Specificity.Position does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[94,72] package Specificity.Position does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[95,100] package Specificity.Position does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[110,23] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[123,44] package Specificity.Position does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[125,44] package Specificity.Position does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemModification.java:[143,18] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.xtandem_parser.XTandemModification [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[58,22] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[75,23] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[82,23] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[87,23] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[93,23] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[108,23] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[114,23] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[121,23] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[125,23] cannot find symbol [ERROR] symbol: class ParameterExtractionException [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[127,9] cannot find symbol [ERROR] symbol: class DigestionPreferences [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[127,55] cannot find symbol [ERROR] symbol: class DigestionPreferences [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.XTandemParametersExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/XTandemParametersExtractor.java:[130,69] package DigestionPreferences does not exist [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemEnzyme.java:[47,63] no suitable constructor found for Enzyme(java.lang.String) [ERROR] constructor com.compomics.util.experiment.biology.Enzyme.Enzyme(int,java.lang.String,java.lang.String,java.lang.String,java.lang.String,java.lang.String) is not applicable [ERROR] (actual and formal argument lists differ in length) [ERROR] constructor com.compomics.util.experiment.biology.Enzyme.Enzyme(int,java.lang.String,java.lang.String,java.lang.String,java.lang.String,java.lang.String,java.lang.Boolean,java.lang.Boolean) is not applicable [ERROR] (actual and formal argument lists differ in length) [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemEnzyme.java:[50,23] cannot find symbol [ERROR] symbol: method addAminoAcidBefore(java.lang.Character) [ERROR] location: variable enzyme of type com.compomics.util.experiment.biology.Enzyme [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemEnzyme.java:[53,23] cannot find symbol [ERROR] symbol: method addRestrictionAfter(java.lang.Character) [ERROR] location: variable enzyme of type com.compomics.util.experiment.biology.Enzyme [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/xtandem_parser/XTandemEnzyme.java:[54,15] cannot find symbol [ERROR] symbol: method setCvTerm(com.compomics.util.pride.CvTerm) [ERROR] location: variable enzyme of type com.compomics.util.experiment.biology.Enzyme [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[109,9] cannot find symbol [ERROR] symbol: class FileParameterExtractor [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[112,33] cannot find symbol [ERROR] symbol: class FileParameterExtractor [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideXMLParameterExtractor.java:[114,33] cannot find symbol [ERROR] symbol: class FileParameterExtractor [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideXMLParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[109,9] cannot find symbol [ERROR] symbol: class FileParameterExtractor [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[112,34] cannot find symbol [ERROR] symbol: class FileParameterExtractor [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] /my/path/PRIDEParametersExtractor/src/main/java/com/compomics/pridesearchparameterextractor/extraction/impl/PrideMzIDParameterExtractor.java:[114,34] cannot find symbol [ERROR] symbol: class FileParameterExtractor [ERROR] location: class com.compomics.pridesearchparameterextractor.extraction.impl.PrideMzIDParameterExtractor [ERROR] -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
alephreish commented 6 years ago

Installing the 2.0.0-SNAPSHOT version of pride-asa-pipeline from the PRIDE-Toolsuite's fork https://github.com/PRIDE-Toolsuite/pride-asa-pipeline has the same effect: the offending classes do not seem to be defined there either.

ypriverol commented 6 years ago

Dear Alexander:

This is an internal pride project in collaboration with other two groups. Is still under development and we haven’t put much efforts to make it available for external users. I will put some time today to clean the code and the project and build all the dependencies.

alephreish commented 6 years ago

@ypriverol

I see. Thanks for finding the time to make the repository more user friendly!

I'm trying to approach the same problem as described here: https://github.com/compomics/peptide-shaker/issues/278 and PRIDEParametersExtractor was mentioned there.