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
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject "unsubscribe" to
[EMAIL PROTECTED]
