Dear Zong-Pei,
I'll post an answer on the base-devel list.
Cheers,
Kjell
[EMAIL PROTECTED] wrote:
>Dear All,
>
>Our attempt to install the latest CVS of BASE1 (1.2.17 something
>which is downloaded today) on an Opteron box has been unsuccessful.
>Here're some background information:
>
>$ uname -a
>Linux xxxxxx 2.6.16-1.2069_FC4smp #1 SMP Tue Mar 28 12:48:20 EST 2006
>x86_64 x86_64 x86_64 GNU/Linux
>
>$ gcc --version
>gcc (GCC) 4.0.2 20051125 (Red Hat 4.0.2-8)
>
>$ java -version
>java version "1.4.2"
>gij (GNU libgcj) version 4.0.2 20051125 (Red Hat 4.0.2-8)
>
>$javac -v
>Eclipse Java Compiler v_579_R31x, 3.1.1 release
>
>
>The warning and error messages are enclosed below.
>Your comments and suggestions are much appreciated.
>
>...
>make[3]: Entering directory
>`/usr/local/source_code/Linux/BASE/base-1.2.17b-cvs/src/jobRunner'
>if gcc -DHAVE_CONFIG_H -I. -I. -I../.. -DJOBRUNNER_USER_UID=6000
>-DBASE_USER_UID=6000 -Wall -O3 -MT jobRunner-jobRunner.o -MD -MP -MF
>".deps/jobRunner-jobRunner.Tpo" -c -o jobRunner-jobRunner.o `test -f
>'jobRunner.c' || echo './'`jobRunner.c; \
>then mv -f ".deps/jobRunner-jobRunner.Tpo" ".deps/jobRunner-jobRunner.Po";
>else rm -f ".deps/jobRunner-jobRunner.Tpo"; exit 1; fi
>gcc -Wall -O3 -o jobRunner jobRunner-jobRunner.o
>make[3]: Leaving directory
>`/usr/local/source_code/Linux/BASE/base-1.2.17b-cvs/src/jobRunner'
>Making all in mageml
>make[3]: Entering directory
>`/usr/local/source_code/Linux/BASE/base-1.2.17b-cvs/src/mageml'
>javac -d . -classpath
>.:./../../include/java/MAGEstk-current.jar:./../../include/java/baseDNR.jar:./../../include/java/iText.jar:./../../include/java/xercesImpl.jar:
> ./ArrayDesign_package_BASE.java ./ArrayManufacture_BASE.java
>./Array_BASE.java ./Array_package_BASE.java
>./AuditAndSecurity_package_BASE.java ./BASEutils.java
>./BioAssayData_package_BASE.java ./BioAssay_package_BASE.java
>./BioDataCube_BASE.java ./BioMaterial_package_BASE.java ./BioSample_BASE.java
>./BioSequence_BASE.java ./BioSequence_package_BASE.java ./BioSource_BASE.java
>./Channel_BASE.java ./Compound_BASE.java ./DOMValidator.java
>./Database_BASE.java ./DerivedBioAssay_BASE.java
>./Description_package_BASE.java ./DesignElement_package_BASE.java
>./ExperimentDesign_BASE.java ./Experiment_BASE.java
>./Experiment_package_BASE.java ./FeatureDimension_BASE.java
>./FeatureExtraction_BASE.java ./FeatureReporterMap_BASE.java
>./Feature_BASE.java ./Hardware_BASE.java ./Hybridization_BASE.java
>./ImageAcquisition_BASE.java .
/Image_BASE.java ./LabeledExtract_BASE.java ./MeasuredBioAssayData_BASE.java
./MeasuredBioAssay_BASE.java ./MyErrorHandler.java ./Person_BASE.java
./PhysicalArrayDesign_BASE.java ./PhysicalBioAssay_BASE.java
./Protocol_BASE.java ./Protocol_package_BASE.java
./QuantitationTypeDimension_BASE.java ./QuantitationType_package_BASE.java
./Reporter_BASE.java ./SaxHandler.java ./Software_BASE.java ./Zone_BASE.java
./exportMAGEML.java && \
>jar cf base_to_mageml.jar *.class
>----------
>1. WARNING in ./ArrayDesign_package_BASE.java
> (at line 8)
> public class ArrayDesign_package_BASE extends ArrayDesign_package
> ^^^^^^^^^^^^^^^^^^^^^^^^
>The serializable class ArrayDesign_package_BASE does not declare a static
>final serialVersionUID field of type long
>----------
>----------
>2. WARNING in ./ArrayManufacture_BASE.java
> (at line 2)
> import java.util.Date;
> ^^^^^^^^^^^^^^
>The import java.util.Date is never used
>----------
>----------
>3. WARNING in ./ArrayManufacture_BASE.java
> (at line 3)
> import java.text.DateFormat;
> ^^^^^^^^^^^^^^^^^^^^
>The import java.text.DateFormat is never used
>----------
>----------
>4. WARNING in ./ArrayManufacture_BASE.java
> (at line 14)
> public class ArrayManufacture_BASE extends ArrayManufacture
> ^^^^^^^^^^^^^^^^^^^^^
>The serializable class ArrayManufacture_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>5. WARNING in ./Array_BASE.java
> (at line 2)
> import java.text.DateFormat;
> ^^^^^^^^^^^^^^^^^^^^
>The import java.text.DateFormat is never used
>----------
>----------
>6. WARNING in ./Array_BASE.java
> (at line 9)
> import org.biomage.AuditAndSecurity.Person;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Person is never used
>----------
>----------
>7. WARNING in ./Array_BASE.java
> (at line 10)
> import org.biomage.AuditAndSecurity.Audit;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Audit is never used
>----------
>----------
>8. WARNING in ./Array_BASE.java
> (at line 16)
> public class Array_BASE extends Array
> ^^^^^^^^^^
>The serializable class Array_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>9. WARNING in ./Array_package_BASE.java
> (at line 8)
> public class Array_package_BASE extends Array_package
> ^^^^^^^^^^^^^^^^^^
>The serializable class Array_package_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>10. WARNING in ./AuditAndSecurity_package_BASE.java
> (at line 7)
> public class AuditAndSecurity_package_BASE extends
> AuditAndSecurity_package
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The serializable class AuditAndSecurity_package_BASE does not declare a static
>final serialVersionUID field of type long
>----------
>----------
>11. WARNING in ./BASEutils.java
> (at line 391)
> boolean dyeSwap = false;
> ^^^^^^^
>The local variable dyeSwap is never read
>----------
>----------
>12. WARNING in ./BASEutils.java
> (at line 718)
> NodeList nl = topp.getChildNodes();
> ^^
>The local variable nl is never read
>----------
>----------
>13. WARNING in ./BASEutils.java
> (at line 1047)
> long tid = System.currentTimeMillis();
> ^^^
>The local variable tid is never read
>----------
>----------
>14. WARNING in ./BASEutils.java
> (at line 1362)
> private static void quickfix1(Document document, String fixname)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The method quickfix1(Document, String) from the type BASEutils is never used
>locally
>----------
>----------
>15. WARNING in ./BASEutils.java
> (at line 1422)
> Document document = null;
> ^^^^^^^^
>The local variable document is never read
>----------
>----------
>16. WARNING in ./BASEutils.java
> (at line 1920)
> String value = (String) values.get(key);
> ^^^^^
>The local variable value is never read
>----------
>----------
>17. WARNING in ./BioAssayData_package_BASE.java
> (at line 22)
> public class BioAssayData_package_BASE extends BioAssayData_package
> ^^^^^^^^^^^^^^^^^^^^^^^^^
>The serializable class BioAssayData_package_BASE does not declare a static
>final serialVersionUID field of type long
>----------
>----------
>18. WARNING in ./BioAssayData_package_BASE.java
> (at line 313)
> int tmp = result.getInt("target");
> ^^^
>The local variable tmp is never read
>----------
>----------
>19. WARNING in ./BioAssayData_package_BASE.java
> (at line 384)
> int dbaId = result.getInt("dbaid");
> ^^^^^
>The local variable dbaId is never read
>----------
>----------
>20. WARNING in ./BioAssay_package_BASE.java
> (at line 8)
> import org.biomage.BioAssay.PhysicalBioAssay;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioAssay.PhysicalBioAssay is never used
>----------
>----------
>21. WARNING in ./BioAssay_package_BASE.java
> (at line 16)
> public class BioAssay_package_BASE extends BioAssay_package
> ^^^^^^^^^^^^^^^^^^^^^
>The serializable class BioAssay_package_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>22. WARNING in ./BioAssay_package_BASE.java
> (at line 346)
> String imaName = result.getString("name");
> ^^^^^^^
>The local variable imaName is never read
>----------
>----------
>23. WARNING in ./BioDataCube_BASE.java
> (at line 2)
> import java.io.Writer;
> ^^^^^^^^^^^^^^
>The import java.io.Writer is never used
>----------
>----------
>24. WARNING in ./BioDataCube_BASE.java
> (at line 12)
> import org.biomage.BioAssay.MeasuredBioAssay;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioAssay.MeasuredBioAssay is never used
>----------
>----------
>25. WARNING in ./BioDataCube_BASE.java
> (at line 13)
> import org.biomage.BioAssayData.FeatureDimension;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioAssayData.FeatureDimension is never used
>----------
>----------
>26. WARNING in ./BioDataCube_BASE.java
> (at line 22)
> public class BioDataCube_BASE extends BioDataCube
> ^^^^^^^^^^^^^^^^
>The serializable class BioDataCube_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>27. WARNING in ./BioDataCube_BASE.java
> (at line 26)
> private BioAssayDimension bioAssayDimension;
> ^^^^^^^^^^^^^^^^^
>The field BioDataCube_BASE.bioAssayDimension is never read locally
>----------
>----------
>28. WARNING in ./BioDataCube_BASE.java
> (at line 27)
> private QuantitationTypeDimension quantitationTypeDimension;
> ^^^^^^^^^^^^^^^^^^^^^^^^^
>The field BioDataCube_BASE.quantitationTypeDimension is never read locally
>----------
>----------
>29. WARNING in ./BioDataCube_BASE.java
> (at line 28)
> private DesignElementDimension designElementDimension;
> ^^^^^^^^^^^^^^^^^^^^^^
>The field BioDataCube_BASE.designElementDimension is never read locally
>----------
>----------
>30. WARNING in ./BioMaterial_package_BASE.java
> (at line 11)
> public class BioMaterial_package_BASE extends BioMaterial_package
> ^^^^^^^^^^^^^^^^^^^^^^^^
>The serializable class BioMaterial_package_BASE does not declare a static
>final serialVersionUID field of type long
>----------
>----------
>31. WARNING in ./BioSample_BASE.java
> (at line 2)
> import java.util.Date;
> ^^^^^^^^^^^^^^
>The import java.util.Date is never used
>----------
>----------
>32. WARNING in ./BioSample_BASE.java
> (at line 3)
> import java.text.DateFormat;
> ^^^^^^^^^^^^^^^^^^^^
>The import java.text.DateFormat is never used
>----------
>----------
>33. WARNING in ./BioSample_BASE.java
> (at line 14)
> import org.biomage.BioMaterial.Compound;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioMaterial.Compound is never used
>----------
>----------
>34. WARNING in ./BioSample_BASE.java
> (at line 17)
> import org.biomage.AuditAndSecurity.Audit;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Audit is never used
>----------
>----------
>35. WARNING in ./BioSample_BASE.java
> (at line 21)
> import org.biomage.Common.NameValueType;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.Common.NameValueType is never used
>----------
>----------
>36. WARNING in ./BioSample_BASE.java
> (at line 26)
> public class BioSample_BASE extends BioSample
> ^^^^^^^^^^^^^^
>The serializable class BioSample_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>37. WARNING in ./BioSequence_BASE.java
> (at line 7)
> import org.biomage.Description.DatabaseEntry;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.Description.DatabaseEntry is never used
>----------
>----------
>38. WARNING in ./BioSequence_BASE.java
> (at line 8)
> import org.biomage.Description.Database;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.Description.Database is never used
>----------
>----------
>39. WARNING in ./BioSequence_BASE.java
> (at line 14)
> public class BioSequence_BASE extends BioSequence
> ^^^^^^^^^^^^^^^^
>The serializable class BioSequence_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>40. WARNING in ./BioSequence_BASE.java
> (at line 122)
> OntologyEntry oe=null;
> ^^
>The local variable oe is never read
>----------
>----------
>41. WARNING in ./BioSequence_package_BASE.java
> (at line 7)
> public class BioSequence_package_BASE extends BioSequence_package
> ^^^^^^^^^^^^^^^^^^^^^^^^
>The serializable class BioSequence_package_BASE does not declare a static
>final serialVersionUID field of type long
>----------
>----------
>42. WARNING in ./BioSource_BASE.java
> (at line 2)
> import java.util.Date;
> ^^^^^^^^^^^^^^
>The import java.util.Date is never used
>----------
>----------
>43. WARNING in ./BioSource_BASE.java
> (at line 3)
> import java.text.DateFormat;
> ^^^^^^^^^^^^^^^^^^^^
>The import java.text.DateFormat is never used
>----------
>----------
>44. WARNING in ./BioSource_BASE.java
> (at line 9)
> import org.biomage.AuditAndSecurity.Person;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Person is never used
>----------
>----------
>45. WARNING in ./BioSource_BASE.java
> (at line 10)
> import org.biomage.AuditAndSecurity.Audit;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Audit is never used
>----------
>----------
>46. WARNING in ./BioSource_BASE.java
> (at line 17)
> public class BioSource_BASE extends BioSource
> ^^^^^^^^^^^^^^
>The serializable class BioSource_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>47. WARNING in ./Channel_BASE.java
> (at line 1)
> import java.sql.*;
> ^^^^^^^^
>The import java.sql is never used
>----------
>----------
>48. WARNING in ./Channel_BASE.java
> (at line 2)
> import java.util.Date;
> ^^^^^^^^^^^^^^
>The import java.util.Date is never used
>----------
>----------
>49. WARNING in ./Channel_BASE.java
> (at line 3)
> import java.text.DateFormat;
> ^^^^^^^^^^^^^^^^^^^^
>The import java.text.DateFormat is never used
>----------
>----------
>50. WARNING in ./Channel_BASE.java
> (at line 9)
> import org.biomage.AuditAndSecurity.Person;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Person is never used
>----------
>----------
>51. WARNING in ./Channel_BASE.java
> (at line 10)
> import org.biomage.AuditAndSecurity.Audit;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Audit is never used
>----------
>----------
>52. WARNING in ./Channel_BASE.java
> (at line 12)
> import org.biomage.BioMaterial.BioMaterial_package;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioMaterial.BioMaterial_package is never used
>----------
>----------
>53. WARNING in ./Channel_BASE.java
> (at line 14)
> public class Channel_BASE extends Channel
> ^^^^^^^^^^^^
>The serializable class Channel_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>54. WARNING in ./Channel_BASE.java
> (at line 35)
> String q=new String();
> ^
>The local variable q is never read
>----------
>----------
>55. WARNING in ./Compound_BASE.java
> (at line 9)
> import org.biomage.AuditAndSecurity.Person;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Person is never used
>----------
>----------
>56. WARNING in ./Compound_BASE.java
> (at line 10)
> import org.biomage.AuditAndSecurity.Audit;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Audit is never used
>----------
>----------
>57. WARNING in ./Compound_BASE.java
> (at line 11)
> import org.biomage.Protocol.Protocol;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.Protocol.Protocol is never used
>----------
>----------
>58. WARNING in ./Compound_BASE.java
> (at line 14)
> public class Compound_BASE extends Compound
> ^^^^^^^^^^^^^
>The serializable class Compound_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>59. WARNING in ./DOMValidator.java
> (at line 21)
> Document doc = builder.parse(new File(args[0]) );
> ^^^
>The local variable doc is never read
>----------
>----------
>60. WARNING in ./Database_BASE.java
> (at line 1)
> import java.sql.*;
> ^^^^^^^^
>The import java.sql is never used
>----------
>----------
>61. WARNING in ./Database_BASE.java
> (at line 8)
> public class Database_BASE extends Database
> ^^^^^^^^^^^^^
>The serializable class Database_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>62. WARNING in ./DerivedBioAssay_BASE.java
> (at line 1)
> import java.util.Date;
> ^^^^^^^^^^^^^^
>The import java.util.Date is never used
>----------
>----------
>63. WARNING in ./DerivedBioAssay_BASE.java
> (at line 2)
> import java.text.DateFormat;
> ^^^^^^^^^^^^^^^^^^^^
>The import java.text.DateFormat is never used
>----------
>----------
>64. WARNING in ./DerivedBioAssay_BASE.java
> (at line 7)
> import org.biomage.AuditAndSecurity.Audit;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Audit is never used
>----------
>----------
>65. WARNING in ./DerivedBioAssay_BASE.java
> (at line 8)
> import org.biomage.AuditAndSecurity.Person;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Person is never used
>----------
>----------
>66. WARNING in ./DerivedBioAssay_BASE.java
> (at line 10)
> import org.biomage.BioAssay.BioAssay_package;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioAssay.BioAssay_package is never used
>----------
>----------
>67. WARNING in ./DerivedBioAssay_BASE.java
> (at line 11)
> import org.biomage.BioAssay.Channel;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioAssay.Channel is never used
>----------
>----------
>68. WARNING in ./DerivedBioAssay_BASE.java
> (at line 12)
> import org.biomage.BioAssayData.DerivedBioAssayData;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioAssayData.DerivedBioAssayData is never used
>----------
>----------
>69. WARNING in ./DerivedBioAssay_BASE.java
> (at line 15)
> public class DerivedBioAssay_BASE extends DerivedBioAssay
> ^^^^^^^^^^^^^^^^^^^^
>The serializable class DerivedBioAssay_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>70. WARNING in ./Description_package_BASE.java
> (at line 6)
> public class Description_package_BASE extends Description_package
> ^^^^^^^^^^^^^^^^^^^^^^^^
>The serializable class Description_package_BASE does not declare a static
>final serialVersionUID field of type long
>----------
>----------
>71. WARNING in ./DesignElement_package_BASE.java
> (at line 8)
> public class DesignElement_package_BASE extends DesignElement_package
> ^^^^^^^^^^^^^^^^^^^^^^^^^^
>The serializable class DesignElement_package_BASE does not declare a static
>final serialVersionUID field of type long
>----------
>----------
>72. WARNING in ./ExperimentDesign_BASE.java
> (at line 2)
> import java.util.Date;
> ^^^^^^^^^^^^^^
>The import java.util.Date is never used
>----------
>----------
>73. WARNING in ./ExperimentDesign_BASE.java
> (at line 3)
> import java.text.DateFormat;
> ^^^^^^^^^^^^^^^^^^^^
>The import java.text.DateFormat is never used
>----------
>----------
>74. WARNING in ./ExperimentDesign_BASE.java
> (at line 12)
> import org.biomage.Description.Description;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.Description.Description is never used
>----------
>----------
>75. WARNING in ./ExperimentDesign_BASE.java
> (at line 13)
> import org.biomage.tools.ontology.MGEDOntologyClassEntry;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.tools.ontology.MGEDOntologyClassEntry is never used
>----------
>----------
>76. WARNING in ./ExperimentDesign_BASE.java
> (at line 15)
> public class ExperimentDesign_BASE extends ExperimentDesign
> ^^^^^^^^^^^^^^^^^^^^^
>The serializable class ExperimentDesign_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>77. WARNING in ./Experiment_BASE.java
> (at line 12)
> import org.biomage.Common.NameValueType;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.Common.NameValueType is never used
>----------
>----------
>78. WARNING in ./Experiment_BASE.java
> (at line 15)
> public class Experiment_BASE extends Experiment
> ^^^^^^^^^^^^^^^
>The serializable class Experiment_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>79. WARNING in ./Experiment_package_BASE.java
> (at line 7)
> public class Experiment_package_BASE extends Experiment_package
> ^^^^^^^^^^^^^^^^^^^^^^^
>The serializable class Experiment_package_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>80. WARNING in ./FeatureDimension_BASE.java
> (at line 2)
> import java.util.Vector;
> ^^^^^^^^^^^^^^^^
>The import java.util.Vector is never used
>----------
>----------
>81. WARNING in ./FeatureDimension_BASE.java
> (at line 7)
> import org.biomage.ArrayDesign.ArrayDesign_package;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.ArrayDesign.ArrayDesign_package is never used
>----------
>----------
>82. WARNING in ./FeatureDimension_BASE.java
> (at line 12)
> public class FeatureDimension_BASE extends FeatureDimension
> ^^^^^^^^^^^^^^^^^^^^^
>The serializable class FeatureDimension_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>83. WARNING in ./FeatureExtraction_BASE.java
> (at line 2)
> import java.util.Date;
> ^^^^^^^^^^^^^^
>The import java.util.Date is never used
>----------
>----------
>84. WARNING in ./FeatureExtraction_BASE.java
> (at line 3)
> import java.text.DateFormat;
> ^^^^^^^^^^^^^^^^^^^^
>The import java.text.DateFormat is never used
>----------
>----------
>85. WARNING in ./FeatureExtraction_BASE.java
> (at line 11)
> import org.biomage.AuditAndSecurity.Audit;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Audit is never used
>----------
>----------
>86. WARNING in ./FeatureExtraction_BASE.java
> (at line 12)
> import org.biomage.BioMaterial.Compound;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioMaterial.Compound is never used
>----------
>----------
>87. WARNING in ./FeatureExtraction_BASE.java
> (at line 13)
> import org.biomage.BioMaterial.BioMaterial_package;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioMaterial.BioMaterial_package is never used
>----------
>----------
>88. WARNING in ./FeatureExtraction_BASE.java
> (at line 19)
> public class FeatureExtraction_BASE extends FeatureExtraction
> ^^^^^^^^^^^^^^^^^^^^^^
>The serializable class FeatureExtraction_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>89. WARNING in ./FeatureReporterMap_BASE.java
> (at line 1)
> import java.sql.*;
> ^^^^^^^^
>The import java.sql is never used
>----------
>----------
>90. WARNING in ./FeatureReporterMap_BASE.java
> (at line 8)
> public class FeatureReporterMap_BASE extends FeatureReporterMap
> ^^^^^^^^^^^^^^^^^^^^^^^
>The serializable class FeatureReporterMap_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>91. WARNING in ./Feature_BASE.java
> (at line 9)
> import org.biomage.DesignElement.DesignElement_package;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.DesignElement.DesignElement_package is never used
>----------
>----------
>92. WARNING in ./Feature_BASE.java
> (at line 10)
> import org.biomage.ArrayDesign.FeatureGroup;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.ArrayDesign.FeatureGroup is never used
>----------
>----------
>93. WARNING in ./Feature_BASE.java
> (at line 11)
> import org.biomage.Description.Description;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.Description.Description is never used
>----------
>----------
>94. WARNING in ./Feature_BASE.java
> (at line 14)
> public class Feature_BASE extends Feature
> ^^^^^^^^^^^^
>The serializable class Feature_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>95. WARNING in ./Hardware_BASE.java
> (at line 2)
> import java.util.Date;
> ^^^^^^^^^^^^^^
>The import java.util.Date is never used
>----------
>----------
>96. WARNING in ./Hardware_BASE.java
> (at line 3)
> import java.text.DateFormat;
> ^^^^^^^^^^^^^^^^^^^^
>The import java.text.DateFormat is never used
>----------
>----------
>97. WARNING in ./Hardware_BASE.java
> (at line 8)
> import org.biomage.AuditAndSecurity.Person;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Person is never used
>----------
>----------
>98. WARNING in ./Hardware_BASE.java
> (at line 9)
> import org.biomage.AuditAndSecurity.Audit;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Audit is never used
>----------
>----------
>99. WARNING in ./Hardware_BASE.java
> (at line 12)
> public class Hardware_BASE extends Hardware
> ^^^^^^^^^^^^^
>The serializable class Hardware_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>100. WARNING in ./Hybridization_BASE.java
> (at line 2)
> import java.util.Date;
> ^^^^^^^^^^^^^^
>The import java.util.Date is never used
>----------
>----------
>101. WARNING in ./Hybridization_BASE.java
> (at line 3)
> import java.text.DateFormat;
> ^^^^^^^^^^^^^^^^^^^^
>The import java.text.DateFormat is never used
>----------
>----------
>102. WARNING in ./Hybridization_BASE.java
> (at line 14)
> import org.biomage.AuditAndSecurity.Audit;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Audit is never used
>----------
>----------
>103. WARNING in ./Hybridization_BASE.java
> (at line 15)
> import org.biomage.BioMaterial.Compound;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioMaterial.Compound is never used
>----------
>----------
>104. WARNING in ./Hybridization_BASE.java
> (at line 16)
> import org.biomage.BioMaterial.BioMaterial_package;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioMaterial.BioMaterial_package is never used
>----------
>----------
>105. WARNING in ./Hybridization_BASE.java
> (at line 20)
> import org.biomage.Array.Array_package;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.Array.Array_package is never used
>----------
>----------
>106. WARNING in ./Hybridization_BASE.java
> (at line 22)
> import org.biomage.Common.NameValueType;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.Common.NameValueType is never used
>----------
>----------
>107. WARNING in ./Hybridization_BASE.java
> (at line 24)
> public class Hybridization_BASE extends Hybridization
> ^^^^^^^^^^^^^^^^^^
>The serializable class Hybridization_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>108. WARNING in ./ImageAcquisition_BASE.java
> (at line 2)
> import java.util.Date;
> ^^^^^^^^^^^^^^
>The import java.util.Date is never used
>----------
>----------
>109. WARNING in ./ImageAcquisition_BASE.java
> (at line 3)
> import java.text.DateFormat;
> ^^^^^^^^^^^^^^^^^^^^
>The import java.text.DateFormat is never used
>----------
>----------
>110. WARNING in ./ImageAcquisition_BASE.java
> (at line 10)
> import org.biomage.AuditAndSecurity.Audit;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Audit is never used
>----------
>----------
>111. WARNING in ./ImageAcquisition_BASE.java
> (at line 17)
> public class ImageAcquisition_BASE extends ImageAcquisition
> ^^^^^^^^^^^^^^^^^^^^^
>The serializable class ImageAcquisition_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>112. WARNING in ./Image_BASE.java
> (at line 2)
> import java.util.Date;
> ^^^^^^^^^^^^^^
>The import java.util.Date is never used
>----------
>----------
>113. WARNING in ./Image_BASE.java
> (at line 3)
> import java.text.DateFormat;
> ^^^^^^^^^^^^^^^^^^^^
>The import java.text.DateFormat is never used
>----------
>----------
>114. WARNING in ./Image_BASE.java
> (at line 9)
> import org.biomage.AuditAndSecurity.Person;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Person is never used
>----------
>----------
>115. WARNING in ./Image_BASE.java
> (at line 10)
> import org.biomage.AuditAndSecurity.Audit;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Audit is never used
>----------
>----------
>116. WARNING in ./Image_BASE.java
> (at line 14)
> public class Image_BASE extends Image
> ^^^^^^^^^^
>The serializable class Image_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>117. WARNING in ./LabeledExtract_BASE.java
> (at line 2)
> import java.util.Date;
> ^^^^^^^^^^^^^^
>The import java.util.Date is never used
>----------
>----------
>118. WARNING in ./LabeledExtract_BASE.java
> (at line 3)
> import java.text.DateFormat;
> ^^^^^^^^^^^^^^^^^^^^
>The import java.text.DateFormat is never used
>----------
>----------
>119. WARNING in ./LabeledExtract_BASE.java
> (at line 14)
> import org.biomage.AuditAndSecurity.Audit;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Audit is never used
>----------
>----------
>120. WARNING in ./LabeledExtract_BASE.java
> (at line 21)
> import org.biomage.Common.NameValueType;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.Common.NameValueType is never used
>----------
>----------
>121. WARNING in ./LabeledExtract_BASE.java
> (at line 26)
> public class LabeledExtract_BASE extends LabeledExtract
> ^^^^^^^^^^^^^^^^^^^
>The serializable class LabeledExtract_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>122. WARNING in ./MeasuredBioAssayData_BASE.java
> (at line 10)
> import org.biomage.BioAssayData.DesignElementDimension;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioAssayData.DesignElementDimension is never used
>----------
>----------
>123. WARNING in ./MeasuredBioAssayData_BASE.java
> (at line 12)
> public class MeasuredBioAssayData_BASE extends MeasuredBioAssayData
> ^^^^^^^^^^^^^^^^^^^^^^^^^
>The serializable class MeasuredBioAssayData_BASE does not declare a static
>final serialVersionUID field of type long
>----------
>----------
>124. WARNING in ./MeasuredBioAssay_BASE.java
> (at line 1)
> import java.util.Date;
> ^^^^^^^^^^^^^^
>The import java.util.Date is never used
>----------
>----------
>125. WARNING in ./MeasuredBioAssay_BASE.java
> (at line 2)
> import java.text.DateFormat;
> ^^^^^^^^^^^^^^^^^^^^
>The import java.text.DateFormat is never used
>----------
>----------
>126. WARNING in ./MeasuredBioAssay_BASE.java
> (at line 7)
> import org.biomage.AuditAndSecurity.Audit;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Audit is never used
>----------
>----------
>127. WARNING in ./MeasuredBioAssay_BASE.java
> (at line 8)
> import org.biomage.AuditAndSecurity.Person;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Person is never used
>----------
>----------
>128. WARNING in ./MeasuredBioAssay_BASE.java
> (at line 10)
> import org.biomage.BioAssay.BioAssay_package;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioAssay.BioAssay_package is never used
>----------
>----------
>129. WARNING in ./MeasuredBioAssay_BASE.java
> (at line 11)
> import org.biomage.BioAssay.Channel;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioAssay.Channel is never used
>----------
>----------
>130. WARNING in ./MeasuredBioAssay_BASE.java
> (at line 12)
> import org.biomage.BioAssay.FeatureExtraction;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioAssay.FeatureExtraction is never used
>----------
>----------
>131. WARNING in ./MeasuredBioAssay_BASE.java
> (at line 16)
> public class MeasuredBioAssay_BASE extends MeasuredBioAssay
> ^^^^^^^^^^^^^^^^^^^^^
>The serializable class MeasuredBioAssay_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>132. WARNING in ./Person_BASE.java
> (at line 7)
> public class Person_BASE extends Person
> ^^^^^^^^^^^
>The serializable class Person_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>133. WARNING in ./PhysicalArrayDesign_BASE.java
> (at line 2)
> import java.util.Date;
> ^^^^^^^^^^^^^^
>The import java.util.Date is never used
>----------
>----------
>134. WARNING in ./PhysicalArrayDesign_BASE.java
> (at line 3)
> import java.text.DateFormat;
> ^^^^^^^^^^^^^^^^^^^^
>The import java.text.DateFormat is never used
>----------
>----------
>135. WARNING in ./PhysicalArrayDesign_BASE.java
> (at line 9)
> import org.biomage.ArrayDesign.Zone;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.ArrayDesign.Zone is never used
>----------
>----------
>136. WARNING in ./PhysicalArrayDesign_BASE.java
> (at line 15)
> import org.biomage.DesignElement.Feature;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.DesignElement.Feature is never used
>----------
>----------
>137. WARNING in ./PhysicalArrayDesign_BASE.java
> (at line 17)
> import org.biomage.AuditAndSecurity.Audit;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Audit is never used
>----------
>----------
>138. WARNING in ./PhysicalArrayDesign_BASE.java
> (at line 18)
> import org.biomage.Common.Identifiable;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.Common.Identifiable is never used
>----------
>----------
>139. WARNING in ./PhysicalArrayDesign_BASE.java
> (at line 23)
> import org.biomage.Common.NameValueType;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.Common.NameValueType is never used
>----------
>----------
>140. WARNING in ./PhysicalArrayDesign_BASE.java
> (at line 26)
> public class PhysicalArrayDesign_BASE extends PhysicalArrayDesign
> ^^^^^^^^^^^^^^^^^^^^^^^^
>The serializable class PhysicalArrayDesign_BASE does not declare a static
>final serialVersionUID field of type long
>----------
>----------
>141. WARNING in ./PhysicalBioAssay_BASE.java
> (at line 1)
> import java.util.Date;
> ^^^^^^^^^^^^^^
>The import java.util.Date is never used
>----------
>----------
>142. WARNING in ./PhysicalBioAssay_BASE.java
> (at line 2)
> import java.text.DateFormat;
> ^^^^^^^^^^^^^^^^^^^^
>The import java.text.DateFormat is never used
>----------
>----------
>143. WARNING in ./PhysicalBioAssay_BASE.java
> (at line 3)
> import java.sql.*;
> ^^^^^^^^
>The import java.sql is never used
>----------
>----------
>144. WARNING in ./PhysicalBioAssay_BASE.java
> (at line 7)
> import org.biomage.AuditAndSecurity.Audit;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Audit is never used
>----------
>----------
>145. WARNING in ./PhysicalBioAssay_BASE.java
> (at line 8)
> import org.biomage.AuditAndSecurity.Person;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Person is never used
>----------
>----------
>146. WARNING in ./PhysicalBioAssay_BASE.java
> (at line 10)
> import org.biomage.BioAssay.BioAssay_package;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioAssay.BioAssay_package is never used
>----------
>----------
>147. WARNING in ./PhysicalBioAssay_BASE.java
> (at line 11)
> import org.biomage.BioAssay.Channel;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.BioAssay.Channel is never used
>----------
>----------
>148. WARNING in ./PhysicalBioAssay_BASE.java
> (at line 14)
> public class PhysicalBioAssay_BASE extends PhysicalBioAssay
> ^^^^^^^^^^^^^^^^^^^^^
>The serializable class PhysicalBioAssay_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>149. WARNING in ./Protocol_BASE.java
> (at line 7)
> import org.biomage.AuditAndSecurity.Person;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Person is never used
>----------
>----------
>150. WARNING in ./Protocol_BASE.java
> (at line 8)
> import org.biomage.AuditAndSecurity.Audit;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.AuditAndSecurity.Audit is never used
>----------
>----------
>151. WARNING in ./Protocol_BASE.java
> (at line 11)
> public class Protocol_BASE extends Protocol
> ^^^^^^^^^^^^^
>The serializable class Protocol_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>152. WARNING in ./Protocol_package_BASE.java
> (at line 10)
> public class Protocol_package_BASE extends Protocol_package
> ^^^^^^^^^^^^^^^^^^^^^
>The serializable class Protocol_package_BASE does not declare a static final
>serialVersionUID field of type long
>----------
>----------
>153. WARNING in ./QuantitationTypeDimension_BASE.java
> (at line 1)
> import java.sql.*;
> ^^^^^^^^
>The import java.sql is never used
>----------
>----------
>154. WARNING in ./QuantitationTypeDimension_BASE.java
> (at line 6)
> import org.biomage.QuantitationType.QuantitationType_package;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.QuantitationType.QuantitationType_package is never used
>----------
>----------
>155. WARNING in ./QuantitationTypeDimension_BASE.java
> (at line 14)
> import org.biomage.Description.Description;
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The import org.biomage.Description.Description is never used
>----------
>----------
>156. WARNING in ./QuantitationTypeDimension_BASE.java
> (at line 17)
> public class QuantitationTypeDimension_BASE extends
> QuantitationTypeDimension
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The serializable class QuantitationTypeDimension_BASE does not declare a
>static final serialVersionUID field of type long
>----------
>----------
>157. WARNING in ./QuantitationTypeDimension_BASE.java
> (at line 37)
> String id=BASEutils.getId(identifier);
> ^^
>The local variable id is never read
>----------
>----------
>158. WARNING in ./QuantitationTypeDimension_BASE.java
> (at line 50)
> OntologyEntry oe=null;
> ^^
>The local variable oe is never read
>----------
>----------
>159. WARNING in ./QuantitationType_package_BASE.java
> (at line 14)
> public class QuantitationType_package_BASE extends
> QuantitationType_package
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>The serializable class QuantitationType_package_BASE does not declare a static
>final serialVersionUID field of type long
>----------
>----------
>160. ERROR in ./QuantitationType_package_BASE.java
> (at line 104)
> qt.setIsBackground(false);
> ^^^^^^^^^^^^^^^
>The method setIsBackground(Boolean) in the type QuantitationType is not
>applicable for the arguments (boolean)
>----------
>161. ERROR in ./QuantitationType_package_BASE.java
> (at line 118)
> qt.setIsBackground(false);
> ^^^^^^^^^^^^^^^
>The method setIsBackground(Boolean) in the type QuantitationType is not
>applicable for the arguments (boolean)
>----------
>162. ERROR in ./QuantitationType_package_BASE.java
> (at line 132)
> qt.setIsBackground(false);
> ^^^^^^^^^^^^^^^
>The method setIsBackground(Boolean) in the type QuantitationType is not
>applicable for the arguments (boolean)
>----------
>162 problems (3 errors, 159 warnings)make[3]: *** [base_to_mageml.jar] Error
>255
>make[3]: Leaving directory
>`/usr/local/source_code/Linux/BASE/base-1.2.17b-cvs/src/mageml'
>make[2]: *** [all-recursive] Error 1
>make[2]: Leaving directory
>`/usr/local/source_code/Linux/BASE/base-1.2.17b-cvs/src'
>make[1]: *** [all-recursive] Error 1
>make[1]: Leaving directory `/usr/local/source_code/Linux/BASE/base-1.2.17b-cvs'
>make: *** [all] Error 2
>
>Script done on Fri 02 Jun 2006 15:51:37 BST
>
>
>-------------------------------------
>Dr Zong-Pei Han
>UNIX Systems Administrator
>Computational Biology Research Group
>University of Oxford
>
>Tel: 01865 285731
>http://www.compbio.ox.ac.uk/
>-------------------------------------
>
>------------------------------------------------------------------------
>
>_______________________________________________
>The BASE general discussion mailing list
>[email protected]
>unsubscribe: send a mail with subject "unsubscribe" to
>[EMAIL PROTECTED]
>
>
_______________________________________________
The BASE general discussion mailing list
[email protected]
unsubscribe: send a mail with subject "unsubscribe" to
[EMAIL PROTECTED]
