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From: Jian Lu <jl...@vb...> - 2005-06-27 14:54:18
|
Mike, I did the second run and still failed. The error messages are almost the same. Thanks, Jian Michael Saffitz wrote: >Hi Jian, > >Have you tried running this command a second time? It may be that the jar >was installed on the first run (and not properly loaded in the classpath), >and on the second run it is in the classpath and runs properly. > >It's strange because I believe these lines: > >[WritePropertyFiles] INFO: Recreating GUS-PluginMgr.prop file > >are written using the commons-logging libraries. > >Thanks, and sorry for the difficulties. (Has anyone else on the list >successfully downloaded and installed 3.5?) > >--Mike > >On 6/26/05 4:19 PM, "Jian Lu" <jl...@vb...> wrote: > > > >>Hi Mike, >> >>The commons-logging.jar is in my $GUS_HOME/lib/java. >> >>Jian >> >>Michael Saffitz wrote: >> >> >> >>>Hi Jian, >>> >>>Can you confirm that the commons-logging.jar is in your $GUS_HOME/lib/java >>>(it should have been installed from $PROJECT_HOME/GUS/DBAdmin/lib/java/ >>> >>>Thanks, >>> >>>Mike >>> >>>On 6/25/05 5:02 PM, "Jian Lu" <jl...@vb...> wrote: >>> >>> >>> >>> >>> >>>>I downloaded the official release, followed the installation instruction >>>>and failed to install. Please advise. Thank you. >>>> >>>>build GUS install -append -installDBSchema >>>>[WritePropertyFiles] Jun 25, 2005 3:02:40 PM >>>>org.gusdb.install.WritePropertyFileTask writeInstallProp >>>>[WritePropertyFiles] INFO: Recreating install.prop file >>>>[WritePropertyFiles] Jun 25, 2005 3:02:40 PM >>>>org.gusdb.install.WritePropertyFileTask writePluginProp >>>>[WritePropertyFiles] INFO: Recreating GUS-PluginMgr.prop file >>>> [copy] Copying 1 file to /home/brcgusts/GUS/gus_home/config >>>> [copy] Copying 1 file to /home/brcgusts/GUS/gus_home/config >>>> [echo] . >>>> [echo] Installing CBIL/Bio >>>> [echo] . >>>> [echo] Installing CBIL/CSP >>>> [echo] . >>>> [echo] Installing CBIL/Util >>>> [echo] . >>>> [echo] Installing CBIL/HQ >>>> [echo] . >>>> [echo] Installing CBIL/ObjectMapper >>>> [concat] No existing files and no nested text, doing nothing >>>> [echo] . >>>> [echo] Installing GUS/Supported >>>> [echo] . >>>> [echo] Installing GUS/Community >>>> [echo] . >>>> [echo] Installing GUS/DBAdmin >>>> [echo] . >>>> [echo] Installing GUS/GOPredict >>>> [echo] . >>>> [echo] Installing GUS/Schema >>>>[InstallSchema] Jun 25, 2005 3:02:46 PM >>>>org.gusdb.schema.InstallSchemaTask execute >>>>[InstallSchema] INFO: Reading database from >>>>/home/brcgusts/GUS/project_home/GUS/Schema/gus_schema.xml >>>>[InstallSchema] Jun 25, 2005 3:02:46 PM >>>>org.gusdb.dbadmin.reader.SchemaReader doRead >>>>[InstallSchema] INFO: Reading Database >>>>[InstallSchema] Jun 25, 2005 3:02:46 PM >>>>org.apache.commons.digester.Digester startElement >>>>[InstallSchema] SEVERE: Begin event threw error >>>>[InstallSchema] java.lang.NoClassDefFoundError: >>>>org/apache/commons/logging/LogFactory >>>>[InstallSchema] at >>>> >>>> >>>> >>>> >>>> >>>org.apache.commons.beanutils.ConvertUtilsBean.<init>(ConvertUtilsBean.java:13 >>>0> >>>) >>> >>> >>> >>> >>>>[InstallSchema] at >>>>org.apache.commons.beanutils.BeanUtilsBean.<init>(BeanUtilsBean.java:110) >>>>[InstallSchema] at >>>>org.apache.commons.beanutils.BeanUtilsBean$1.initialValue(BeanUtilsBean.java >>>>:6 >>>>8) >>>>[InstallSchema] at >>>>org.apache.commons.beanutils.ContextClassLoaderLocal.get(ContextClassLoaderL >>>>oc >>>>al.java:80) >>>>[InstallSchema] at >>>> >>>> >>>> >org.apache.commons.beanutils.BeanUtilsBean.getInstance(BeanUtilsBean.java:78>>> >) > > >>>>[InstallSchema] at >>>>org.apache.commons.beanutils.BeanUtils.populate(BeanUtils.java:298) >>>>[InstallSchema] at >>>> >>>> >>>> >>>> >>>> >>>org.apache.commons.digester.SetPropertiesRule.begin(SetPropertiesRule.java:21 >>>7> >>>) >>> >>> >>> >>> >>>>[InstallSchema] at >>>>org.apache.commons.digester.Rule.begin(Rule.java:152) >>>>[InstallSchema] at >>>>org.apache.commons.digester.Digester.startElement(Digester.java:1286) >>>>[InstallSchema] at >>>>org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) >>>>[InstallSchema] at >>>>org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) >>>>[InstallSchema] at >>>>org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unkno >>>>wn >>>>Source) >>>>[InstallSchema] at >>>>org.apache.xerces.impl.XMLDocumentScannerImpl$ContentDispatcher.scanRootElem >>>>en >>>>tHook(Unknown >>>>Source) >>>>[InstallSchema] at >>>>org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatc >>>>he >>>>r.dispatch(Unknown >>>>Source) >>>>[InstallSchema] at >>>>org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown >>>>Source) >>>>[InstallSchema] at >>>>org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) >>>>[InstallSchema] at >>>>org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) >>>>[InstallSchema] at >>>>org.apache.xerces.parsers.XMLParser.parse(Unknown Source) >>>>[InstallSchema] at >>>>org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) >>>>[InstallSchema] at >>>>org.apache.commons.digester.Digester.parse(Digester.java:1591) >>>>[InstallSchema] at >>>>org.gusdb.dbadmin.reader.XMLReader.readDatabase(XMLReader.java:43) >>>>[InstallSchema] at >>>>org.gusdb.dbadmin.reader.SchemaReader.doRead(SchemaReader.java:50) >>>>[InstallSchema] at >>>>org.gusdb.dbadmin.reader.SchemaReader.read(SchemaReader.java:38) >>>>[InstallSchema] at >>>>org.gusdb.schema.InstallSchemaTask.execute(InstallSchemaTask.java:89) >>>>[InstallSchema] at >>>>org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) >>>>[InstallSchema] at org.apache.tools.ant.Task.perform(Task.java:364) >>>>[InstallSchema] at >>>>org.apache.tools.ant.Target.execute(Target.java:341) >>>>[InstallSchema] at >>>>org.apache.tools.ant.Target.performTasks(Target.java:369) >>>>[InstallSchema] at >>>>org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) >>>>[InstallSchema] at >>>>org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckEx >>>>ec >>>>utor.java:37) >>>>[InstallSchema] at >>>>org.apache.tools.ant.Project.executeTargets(Project.java:1068) >>>>[InstallSchema] at >>>>org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:382) >>>>[InstallSchema] at >>>>org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) >>>>[InstallSchema] at org.apache.tools.ant.Task.perform(Task.java:364) >>>>[InstallSchema] at >>>>org.apache.tools.ant.Target.execute(Target.java:341) >>>>[InstallSchema] at >>>>org.apache.tools.ant.Target.performTasks(Target.java:369) >>>>[InstallSchema] at >>>>org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) >>>>[InstallSchema] at >>>>org.apache.tools.ant.Project.executeTarget(Project.java:1185) >>>>[InstallSchema] at >>>>org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.j >>>>av >>>>a:40) >>>>[InstallSchema] at >>>>org.apache.tools.ant.Project.executeTargets(Project.java:1068) >>>>[InstallSchema] at org.apache.tools.ant.Main.runBuild(Main.java:668) >>>>[InstallSchema] at org.apache.tools.ant.Main.startAnt(Main.java:187) >>>>[InstallSchema] at >>>>org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) >>>>[InstallSchema] at >>>>org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) >>>> >>>>BUILD FAILED >>>>/home/brcgusts/GUS/project_home/install/build.xml:28: The following >>>>error occurred while executing this line: >>>>java.lang.NoClassDefFoundError: org/apache/commons/logging/LogFactory >>>> >>>>Total time: 6 seconds >>>> >>>> >>>> >>>> >>>> >>> >>> >>>------------------------------------------------------- >>>SF.Net email is sponsored by: Discover Easy Linux Migration Strategies >>>from IBM. Find simple to follow Roadmaps, straightforward articles, >>>informative Webcasts and more! Get everything you need to get up to >>>speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click >>>_______________________________________________ >>>Gusdev-gusdev mailing list >>>Gus...@li... >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >>> >>> >>> > > > |
|
From: Michael S. <msa...@pc...> - 2005-06-27 14:51:08
|
Hi Jian, Have you tried running this command a second time? It may be that the jar was installed on the first run (and not properly loaded in the classpath), and on the second run it is in the classpath and runs properly. It's strange because I believe these lines: [WritePropertyFiles] INFO: Recreating GUS-PluginMgr.prop file are written using the commons-logging libraries. Thanks, and sorry for the difficulties. (Has anyone else on the list successfully downloaded and installed 3.5?) --Mike On 6/26/05 4:19 PM, "Jian Lu" <jl...@vb...> wrote: > Hi Mike, > > The commons-logging.jar is in my $GUS_HOME/lib/java. > > Jian > > Michael Saffitz wrote: > >> Hi Jian, >> >> Can you confirm that the commons-logging.jar is in your $GUS_HOME/lib/java >> (it should have been installed from $PROJECT_HOME/GUS/DBAdmin/lib/java/ >> >> Thanks, >> >> Mike >> >> On 6/25/05 5:02 PM, "Jian Lu" <jl...@vb...> wrote: >> >> >> >>> I downloaded the official release, followed the installation instruction >>> and failed to install. Please advise. Thank you. >>> >>> build GUS install -append -installDBSchema >>> [WritePropertyFiles] Jun 25, 2005 3:02:40 PM >>> org.gusdb.install.WritePropertyFileTask writeInstallProp >>> [WritePropertyFiles] INFO: Recreating install.prop file >>> [WritePropertyFiles] Jun 25, 2005 3:02:40 PM >>> org.gusdb.install.WritePropertyFileTask writePluginProp >>> [WritePropertyFiles] INFO: Recreating GUS-PluginMgr.prop file >>> [copy] Copying 1 file to /home/brcgusts/GUS/gus_home/config >>> [copy] Copying 1 file to /home/brcgusts/GUS/gus_home/config >>> [echo] . >>> [echo] Installing CBIL/Bio >>> [echo] . >>> [echo] Installing CBIL/CSP >>> [echo] . >>> [echo] Installing CBIL/Util >>> [echo] . >>> [echo] Installing CBIL/HQ >>> [echo] . >>> [echo] Installing CBIL/ObjectMapper >>> [concat] No existing files and no nested text, doing nothing >>> [echo] . >>> [echo] Installing GUS/Supported >>> [echo] . >>> [echo] Installing GUS/Community >>> [echo] . >>> [echo] Installing GUS/DBAdmin >>> [echo] . >>> [echo] Installing GUS/GOPredict >>> [echo] . >>> [echo] Installing GUS/Schema >>> [InstallSchema] Jun 25, 2005 3:02:46 PM >>> org.gusdb.schema.InstallSchemaTask execute >>> [InstallSchema] INFO: Reading database from >>> /home/brcgusts/GUS/project_home/GUS/Schema/gus_schema.xml >>> [InstallSchema] Jun 25, 2005 3:02:46 PM >>> org.gusdb.dbadmin.reader.SchemaReader doRead >>> [InstallSchema] INFO: Reading Database >>> [InstallSchema] Jun 25, 2005 3:02:46 PM >>> org.apache.commons.digester.Digester startElement >>> [InstallSchema] SEVERE: Begin event threw error >>> [InstallSchema] java.lang.NoClassDefFoundError: >>> org/apache/commons/logging/LogFactory >>> [InstallSchema] at >>> >>> >>> >> org.apache.commons.beanutils.ConvertUtilsBean.<init>(ConvertUtilsBean.java:13 >> 0> >> ) >> >> >>> [InstallSchema] at >>> org.apache.commons.beanutils.BeanUtilsBean.<init>(BeanUtilsBean.java:110) >>> [InstallSchema] at >>> org.apache.commons.beanutils.BeanUtilsBean$1.initialValue(BeanUtilsBean.java >>> :6 >>> 8) >>> [InstallSchema] at >>> org.apache.commons.beanutils.ContextClassLoaderLocal.get(ContextClassLoaderL >>> oc >>> al.java:80) >>> [InstallSchema] at >>> org.apache.commons.beanutils.BeanUtilsBean.getInstance(BeanUtilsBean.java:78>>> ) >>> [InstallSchema] at >>> org.apache.commons.beanutils.BeanUtils.populate(BeanUtils.java:298) >>> [InstallSchema] at >>> >>> >>> >> org.apache.commons.digester.SetPropertiesRule.begin(SetPropertiesRule.java:21 >> 7> >> ) >> >> >>> [InstallSchema] at >>> org.apache.commons.digester.Rule.begin(Rule.java:152) >>> [InstallSchema] at >>> org.apache.commons.digester.Digester.startElement(Digester.java:1286) >>> [InstallSchema] at >>> org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) >>> [InstallSchema] at >>> org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) >>> [InstallSchema] at >>> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unkno >>> wn >>> Source) >>> [InstallSchema] at >>> org.apache.xerces.impl.XMLDocumentScannerImpl$ContentDispatcher.scanRootElem >>> en >>> tHook(Unknown >>> Source) >>> [InstallSchema] at >>> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatc >>> he >>> r.dispatch(Unknown >>> Source) >>> [InstallSchema] at >>> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown >>> Source) >>> [InstallSchema] at >>> org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) >>> [InstallSchema] at >>> org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) >>> [InstallSchema] at >>> org.apache.xerces.parsers.XMLParser.parse(Unknown Source) >>> [InstallSchema] at >>> org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) >>> [InstallSchema] at >>> org.apache.commons.digester.Digester.parse(Digester.java:1591) >>> [InstallSchema] at >>> org.gusdb.dbadmin.reader.XMLReader.readDatabase(XMLReader.java:43) >>> [InstallSchema] at >>> org.gusdb.dbadmin.reader.SchemaReader.doRead(SchemaReader.java:50) >>> [InstallSchema] at >>> org.gusdb.dbadmin.reader.SchemaReader.read(SchemaReader.java:38) >>> [InstallSchema] at >>> org.gusdb.schema.InstallSchemaTask.execute(InstallSchemaTask.java:89) >>> [InstallSchema] at >>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) >>> [InstallSchema] at org.apache.tools.ant.Task.perform(Task.java:364) >>> [InstallSchema] at >>> org.apache.tools.ant.Target.execute(Target.java:341) >>> [InstallSchema] at >>> org.apache.tools.ant.Target.performTasks(Target.java:369) >>> [InstallSchema] at >>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) >>> [InstallSchema] at >>> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckEx >>> ec >>> utor.java:37) >>> [InstallSchema] at >>> org.apache.tools.ant.Project.executeTargets(Project.java:1068) >>> [InstallSchema] at >>> org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:382) >>> [InstallSchema] at >>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) >>> [InstallSchema] at org.apache.tools.ant.Task.perform(Task.java:364) >>> [InstallSchema] at >>> org.apache.tools.ant.Target.execute(Target.java:341) >>> [InstallSchema] at >>> org.apache.tools.ant.Target.performTasks(Target.java:369) >>> [InstallSchema] at >>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) >>> [InstallSchema] at >>> org.apache.tools.ant.Project.executeTarget(Project.java:1185) >>> [InstallSchema] at >>> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.j >>> av >>> a:40) >>> [InstallSchema] at >>> org.apache.tools.ant.Project.executeTargets(Project.java:1068) >>> [InstallSchema] at org.apache.tools.ant.Main.runBuild(Main.java:668) >>> [InstallSchema] at org.apache.tools.ant.Main.startAnt(Main.java:187) >>> [InstallSchema] at >>> org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) >>> [InstallSchema] at >>> org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) >>> >>> BUILD FAILED >>> /home/brcgusts/GUS/project_home/install/build.xml:28: The following >>> error occurred while executing this line: >>> java.lang.NoClassDefFoundError: org/apache/commons/logging/LogFactory >>> >>> Total time: 6 seconds >>> >>> >>> >> >> >> >> >> ------------------------------------------------------- >> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies >> from IBM. Find simple to follow Roadmaps, straightforward articles, >> informative Webcasts and more! Get everything you need to get up to >> speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> > |
|
From: Jian Lu <jl...@vb...> - 2005-06-27 08:40:34
|
I downloaded the official release, followed the installation instruction
and failed to install. Please advise. Thank you.
build GUS install -append -installDBSchema
[WritePropertyFiles] Jun 25, 2005 3:02:40 PM
org.gusdb.install.WritePropertyFileTask writeInstallProp
[WritePropertyFiles] INFO: Recreating install.prop file
[WritePropertyFiles] Jun 25, 2005 3:02:40 PM
org.gusdb.install.WritePropertyFileTask writePluginProp
[WritePropertyFiles] INFO: Recreating GUS-PluginMgr.prop file
[copy] Copying 1 file to /home/brcgusts/GUS/gus_home/config
[copy] Copying 1 file to /home/brcgusts/GUS/gus_home/config
[echo] .
[echo] Installing CBIL/Bio
[echo] .
[echo] Installing CBIL/CSP
[echo] .
[echo] Installing CBIL/Util
[echo] .
[echo] Installing CBIL/HQ
[echo] .
[echo] Installing CBIL/ObjectMapper
[concat] No existing files and no nested text, doing nothing
[echo] .
[echo] Installing GUS/Supported
[echo] .
[echo] Installing GUS/Community
[echo] .
[echo] Installing GUS/DBAdmin
[echo] .
[echo] Installing GUS/GOPredict
[echo] .
[echo] Installing GUS/Schema
[InstallSchema] Jun 25, 2005 3:02:46 PM
org.gusdb.schema.InstallSchemaTask execute
[InstallSchema] INFO: Reading database from
/home/brcgusts/GUS/project_home/GUS/Schema/gus_schema.xml
[InstallSchema] Jun 25, 2005 3:02:46 PM
org.gusdb.dbadmin.reader.SchemaReader doRead
[InstallSchema] INFO: Reading Database
[InstallSchema] Jun 25, 2005 3:02:46 PM
org.apache.commons.digester.Digester startElement
[InstallSchema] SEVERE: Begin event threw error
[InstallSchema] java.lang.NoClassDefFoundError:
org/apache/commons/logging/LogFactory
[InstallSchema] at
org.apache.commons.beanutils.ConvertUtilsBean.<init>(ConvertUtilsBean.java:130)
[InstallSchema] at
org.apache.commons.beanutils.BeanUtilsBean.<init>(BeanUtilsBean.java:110)
[InstallSchema] at
org.apache.commons.beanutils.BeanUtilsBean$1.initialValue(BeanUtilsBean.java:68)
[InstallSchema] at
org.apache.commons.beanutils.ContextClassLoaderLocal.get(ContextClassLoaderLocal.java:80)
[InstallSchema] at
org.apache.commons.beanutils.BeanUtilsBean.getInstance(BeanUtilsBean.java:78)
[InstallSchema] at
org.apache.commons.beanutils.BeanUtils.populate(BeanUtils.java:298)
[InstallSchema] at
org.apache.commons.digester.SetPropertiesRule.begin(SetPropertiesRule.java:217)
[InstallSchema] at
org.apache.commons.digester.Rule.begin(Rule.java:152)
[InstallSchema] at
org.apache.commons.digester.Digester.startElement(Digester.java:1286)
[InstallSchema] at
org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)
[InstallSchema] at
org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source)
[InstallSchema] at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown
Source)
[InstallSchema] at
org.apache.xerces.impl.XMLDocumentScannerImpl$ContentDispatcher.scanRootElementHook(Unknown
Source)
[InstallSchema] at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown
Source)
[InstallSchema] at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
Source)
[InstallSchema] at
org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
[InstallSchema] at
org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
[InstallSchema] at
org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
[InstallSchema] at
org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
[InstallSchema] at
org.apache.commons.digester.Digester.parse(Digester.java:1591)
[InstallSchema] at
org.gusdb.dbadmin.reader.XMLReader.readDatabase(XMLReader.java:43)
[InstallSchema] at
org.gusdb.dbadmin.reader.SchemaReader.doRead(SchemaReader.java:50)
[InstallSchema] at
org.gusdb.dbadmin.reader.SchemaReader.read(SchemaReader.java:38)
[InstallSchema] at
org.gusdb.schema.InstallSchemaTask.execute(InstallSchemaTask.java:89)
[InstallSchema] at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275)
[InstallSchema] at org.apache.tools.ant.Task.perform(Task.java:364)
[InstallSchema] at
org.apache.tools.ant.Target.execute(Target.java:341)
[InstallSchema] at
org.apache.tools.ant.Target.performTasks(Target.java:369)
[InstallSchema] at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216)
[InstallSchema] at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:37)
[InstallSchema] at
org.apache.tools.ant.Project.executeTargets(Project.java:1068)
[InstallSchema] at
org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:382)
[InstallSchema] at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275)
[InstallSchema] at org.apache.tools.ant.Task.perform(Task.java:364)
[InstallSchema] at
org.apache.tools.ant.Target.execute(Target.java:341)
[InstallSchema] at
org.apache.tools.ant.Target.performTasks(Target.java:369)
[InstallSchema] at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216)
[InstallSchema] at
org.apache.tools.ant.Project.executeTarget(Project.java:1185)
[InstallSchema] at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40)
[InstallSchema] at
org.apache.tools.ant.Project.executeTargets(Project.java:1068)
[InstallSchema] at org.apache.tools.ant.Main.runBuild(Main.java:668)
[InstallSchema] at org.apache.tools.ant.Main.startAnt(Main.java:187)
[InstallSchema] at
org.apache.tools.ant.launch.Launcher.run(Launcher.java:246)
[InstallSchema] at
org.apache.tools.ant.launch.Launcher.main(Launcher.java:67)
BUILD FAILED
/home/brcgusts/GUS/project_home/install/build.xml:28: The following
error occurred while executing this line:
java.lang.NoClassDefFoundError: org/apache/commons/logging/LogFactory
Total time: 6 seconds
|
|
From: Jian Lu <jl...@vb...> - 2005-06-26 20:19:47
|
Hi Mike, The commons-logging.jar is in my $GUS_HOME/lib/java. Jian Michael Saffitz wrote: >Hi Jian, > >Can you confirm that the commons-logging.jar is in your $GUS_HOME/lib/java >(it should have been installed from $PROJECT_HOME/GUS/DBAdmin/lib/java/ > >Thanks, > >Mike > >On 6/25/05 5:02 PM, "Jian Lu" <jl...@vb...> wrote: > > > >>I downloaded the official release, followed the installation instruction >>and failed to install. Please advise. Thank you. >> >> build GUS install -append -installDBSchema >>[WritePropertyFiles] Jun 25, 2005 3:02:40 PM >>org.gusdb.install.WritePropertyFileTask writeInstallProp >>[WritePropertyFiles] INFO: Recreating install.prop file >>[WritePropertyFiles] Jun 25, 2005 3:02:40 PM >>org.gusdb.install.WritePropertyFileTask writePluginProp >>[WritePropertyFiles] INFO: Recreating GUS-PluginMgr.prop file >> [copy] Copying 1 file to /home/brcgusts/GUS/gus_home/config >> [copy] Copying 1 file to /home/brcgusts/GUS/gus_home/config >> [echo] . >> [echo] Installing CBIL/Bio >> [echo] . >> [echo] Installing CBIL/CSP >> [echo] . >> [echo] Installing CBIL/Util >> [echo] . >> [echo] Installing CBIL/HQ >> [echo] . >> [echo] Installing CBIL/ObjectMapper >> [concat] No existing files and no nested text, doing nothing >> [echo] . >> [echo] Installing GUS/Supported >> [echo] . >> [echo] Installing GUS/Community >> [echo] . >> [echo] Installing GUS/DBAdmin >> [echo] . >> [echo] Installing GUS/GOPredict >> [echo] . >> [echo] Installing GUS/Schema >>[InstallSchema] Jun 25, 2005 3:02:46 PM >>org.gusdb.schema.InstallSchemaTask execute >>[InstallSchema] INFO: Reading database from >>/home/brcgusts/GUS/project_home/GUS/Schema/gus_schema.xml >>[InstallSchema] Jun 25, 2005 3:02:46 PM >>org.gusdb.dbadmin.reader.SchemaReader doRead >>[InstallSchema] INFO: Reading Database >>[InstallSchema] Jun 25, 2005 3:02:46 PM >>org.apache.commons.digester.Digester startElement >>[InstallSchema] SEVERE: Begin event threw error >>[InstallSchema] java.lang.NoClassDefFoundError: >>org/apache/commons/logging/LogFactory >>[InstallSchema] at >> >> >> >org.apache.commons.beanutils.ConvertUtilsBean.<init>(ConvertUtilsBean.java:130> >) > > >>[InstallSchema] at >>org.apache.commons.beanutils.BeanUtilsBean.<init>(BeanUtilsBean.java:110) >>[InstallSchema] at >>org.apache.commons.beanutils.BeanUtilsBean$1.initialValue(BeanUtilsBean.java:6 >>8) >>[InstallSchema] at >>org.apache.commons.beanutils.ContextClassLoaderLocal.get(ContextClassLoaderLoc >>al.java:80) >>[InstallSchema] at >>org.apache.commons.beanutils.BeanUtilsBean.getInstance(BeanUtilsBean.java:78) >>[InstallSchema] at >>org.apache.commons.beanutils.BeanUtils.populate(BeanUtils.java:298) >>[InstallSchema] at >> >> >> >org.apache.commons.digester.SetPropertiesRule.begin(SetPropertiesRule.java:217> >) > > >>[InstallSchema] at >>org.apache.commons.digester.Rule.begin(Rule.java:152) >>[InstallSchema] at >>org.apache.commons.digester.Digester.startElement(Digester.java:1286) >>[InstallSchema] at >>org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) >>[InstallSchema] at >>org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) >>[InstallSchema] at >>org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown >>Source) >>[InstallSchema] at >>org.apache.xerces.impl.XMLDocumentScannerImpl$ContentDispatcher.scanRootElemen >>tHook(Unknown >>Source) >>[InstallSchema] at >>org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatche >>r.dispatch(Unknown >>Source) >>[InstallSchema] at >>org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown >>Source) >>[InstallSchema] at >>org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) >>[InstallSchema] at >>org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) >>[InstallSchema] at >>org.apache.xerces.parsers.XMLParser.parse(Unknown Source) >>[InstallSchema] at >>org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) >>[InstallSchema] at >>org.apache.commons.digester.Digester.parse(Digester.java:1591) >>[InstallSchema] at >>org.gusdb.dbadmin.reader.XMLReader.readDatabase(XMLReader.java:43) >>[InstallSchema] at >>org.gusdb.dbadmin.reader.SchemaReader.doRead(SchemaReader.java:50) >>[InstallSchema] at >>org.gusdb.dbadmin.reader.SchemaReader.read(SchemaReader.java:38) >>[InstallSchema] at >>org.gusdb.schema.InstallSchemaTask.execute(InstallSchemaTask.java:89) >>[InstallSchema] at >>org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) >>[InstallSchema] at org.apache.tools.ant.Task.perform(Task.java:364) >>[InstallSchema] at >>org.apache.tools.ant.Target.execute(Target.java:341) >>[InstallSchema] at >>org.apache.tools.ant.Target.performTasks(Target.java:369) >>[InstallSchema] at >>org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) >>[InstallSchema] at >>org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExec >>utor.java:37) >>[InstallSchema] at >>org.apache.tools.ant.Project.executeTargets(Project.java:1068) >>[InstallSchema] at >>org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:382) >>[InstallSchema] at >>org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) >>[InstallSchema] at org.apache.tools.ant.Task.perform(Task.java:364) >>[InstallSchema] at >>org.apache.tools.ant.Target.execute(Target.java:341) >>[InstallSchema] at >>org.apache.tools.ant.Target.performTasks(Target.java:369) >>[InstallSchema] at >>org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) >>[InstallSchema] at >>org.apache.tools.ant.Project.executeTarget(Project.java:1185) >>[InstallSchema] at >>org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.jav >>a:40) >>[InstallSchema] at >>org.apache.tools.ant.Project.executeTargets(Project.java:1068) >>[InstallSchema] at org.apache.tools.ant.Main.runBuild(Main.java:668) >>[InstallSchema] at org.apache.tools.ant.Main.startAnt(Main.java:187) >>[InstallSchema] at >>org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) >>[InstallSchema] at >>org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) >> >>BUILD FAILED >>/home/brcgusts/GUS/project_home/install/build.xml:28: The following >>error occurred while executing this line: >>java.lang.NoClassDefFoundError: org/apache/commons/logging/LogFactory >> >>Total time: 6 seconds >> >> >> > > > > >------------------------------------------------------- >SF.Net email is sponsored by: Discover Easy Linux Migration Strategies >from IBM. Find simple to follow Roadmaps, straightforward articles, >informative Webcasts and more! Get everything you need to get up to >speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: Michael S. <msa...@pc...> - 2005-06-25 22:28:17
|
Hi Jian, Can you confirm that the commons-logging.jar is in your $GUS_HOME/lib/java (it should have been installed from $PROJECT_HOME/GUS/DBAdmin/lib/java/ Thanks, Mike On 6/25/05 5:02 PM, "Jian Lu" <jl...@vb...> wrote: > I downloaded the official release, followed the installation instruction > and failed to install. Please advise. Thank you. > > build GUS install -append -installDBSchema > [WritePropertyFiles] Jun 25, 2005 3:02:40 PM > org.gusdb.install.WritePropertyFileTask writeInstallProp > [WritePropertyFiles] INFO: Recreating install.prop file > [WritePropertyFiles] Jun 25, 2005 3:02:40 PM > org.gusdb.install.WritePropertyFileTask writePluginProp > [WritePropertyFiles] INFO: Recreating GUS-PluginMgr.prop file > [copy] Copying 1 file to /home/brcgusts/GUS/gus_home/config > [copy] Copying 1 file to /home/brcgusts/GUS/gus_home/config > [echo] . > [echo] Installing CBIL/Bio > [echo] . > [echo] Installing CBIL/CSP > [echo] . > [echo] Installing CBIL/Util > [echo] . > [echo] Installing CBIL/HQ > [echo] . > [echo] Installing CBIL/ObjectMapper > [concat] No existing files and no nested text, doing nothing > [echo] . > [echo] Installing GUS/Supported > [echo] . > [echo] Installing GUS/Community > [echo] . > [echo] Installing GUS/DBAdmin > [echo] . > [echo] Installing GUS/GOPredict > [echo] . > [echo] Installing GUS/Schema > [InstallSchema] Jun 25, 2005 3:02:46 PM > org.gusdb.schema.InstallSchemaTask execute > [InstallSchema] INFO: Reading database from > /home/brcgusts/GUS/project_home/GUS/Schema/gus_schema.xml > [InstallSchema] Jun 25, 2005 3:02:46 PM > org.gusdb.dbadmin.reader.SchemaReader doRead > [InstallSchema] INFO: Reading Database > [InstallSchema] Jun 25, 2005 3:02:46 PM > org.apache.commons.digester.Digester startElement > [InstallSchema] SEVERE: Begin event threw error > [InstallSchema] java.lang.NoClassDefFoundError: > org/apache/commons/logging/LogFactory > [InstallSchema] at > org.apache.commons.beanutils.ConvertUtilsBean.<init>(ConvertUtilsBean.java:130> ) > [InstallSchema] at > org.apache.commons.beanutils.BeanUtilsBean.<init>(BeanUtilsBean.java:110) > [InstallSchema] at > org.apache.commons.beanutils.BeanUtilsBean$1.initialValue(BeanUtilsBean.java:6 > 8) > [InstallSchema] at > org.apache.commons.beanutils.ContextClassLoaderLocal.get(ContextClassLoaderLoc > al.java:80) > [InstallSchema] at > org.apache.commons.beanutils.BeanUtilsBean.getInstance(BeanUtilsBean.java:78) > [InstallSchema] at > org.apache.commons.beanutils.BeanUtils.populate(BeanUtils.java:298) > [InstallSchema] at > org.apache.commons.digester.SetPropertiesRule.begin(SetPropertiesRule.java:217> ) > [InstallSchema] at > org.apache.commons.digester.Rule.begin(Rule.java:152) > [InstallSchema] at > org.apache.commons.digester.Digester.startElement(Digester.java:1286) > [InstallSchema] at > org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) > [InstallSchema] at > org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) > [InstallSchema] at > org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown > Source) > [InstallSchema] at > org.apache.xerces.impl.XMLDocumentScannerImpl$ContentDispatcher.scanRootElemen > tHook(Unknown > Source) > [InstallSchema] at > org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatche > r.dispatch(Unknown > Source) > [InstallSchema] at > org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown > Source) > [InstallSchema] at > org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) > [InstallSchema] at > org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) > [InstallSchema] at > org.apache.xerces.parsers.XMLParser.parse(Unknown Source) > [InstallSchema] at > org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) > [InstallSchema] at > org.apache.commons.digester.Digester.parse(Digester.java:1591) > [InstallSchema] at > org.gusdb.dbadmin.reader.XMLReader.readDatabase(XMLReader.java:43) > [InstallSchema] at > org.gusdb.dbadmin.reader.SchemaReader.doRead(SchemaReader.java:50) > [InstallSchema] at > org.gusdb.dbadmin.reader.SchemaReader.read(SchemaReader.java:38) > [InstallSchema] at > org.gusdb.schema.InstallSchemaTask.execute(InstallSchemaTask.java:89) > [InstallSchema] at > org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) > [InstallSchema] at org.apache.tools.ant.Task.perform(Task.java:364) > [InstallSchema] at > org.apache.tools.ant.Target.execute(Target.java:341) > [InstallSchema] at > org.apache.tools.ant.Target.performTasks(Target.java:369) > [InstallSchema] at > org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) > [InstallSchema] at > org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExec > utor.java:37) > [InstallSchema] at > org.apache.tools.ant.Project.executeTargets(Project.java:1068) > [InstallSchema] at > org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:382) > [InstallSchema] at > org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) > [InstallSchema] at org.apache.tools.ant.Task.perform(Task.java:364) > [InstallSchema] at > org.apache.tools.ant.Target.execute(Target.java:341) > [InstallSchema] at > org.apache.tools.ant.Target.performTasks(Target.java:369) > [InstallSchema] at > org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) > [InstallSchema] at > org.apache.tools.ant.Project.executeTarget(Project.java:1185) > [InstallSchema] at > org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.jav > a:40) > [InstallSchema] at > org.apache.tools.ant.Project.executeTargets(Project.java:1068) > [InstallSchema] at org.apache.tools.ant.Main.runBuild(Main.java:668) > [InstallSchema] at org.apache.tools.ant.Main.startAnt(Main.java:187) > [InstallSchema] at > org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) > [InstallSchema] at > org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) > > BUILD FAILED > /home/brcgusts/GUS/project_home/install/build.xml:28: The following > error occurred while executing this line: > java.lang.NoClassDefFoundError: org/apache/commons/logging/LogFactory > > Total time: 6 seconds > |
|
From: Michael S. <msa...@pc...> - 2005-06-24 17:43:41
|
All,
I'm doing a little bit of post-3.5 cleanup. Changes and notes:
The changes made in the testing-3.5 branch have been merged into the trunk.
We now have 2 "threads" of development:
* trunk is for 3.5.1 development
* branches/pre-3.5 is for 3.0 codebase bug fixes (no new functionality!)
If you want to do "disruptive" development (i.e. new features for a future
release of GUS that is not the next release) then you should branch from the
trunk (or a previous release). If there are bug fixes for 3.5.0, then a new
branch should be created from the release-3.5.0.0 tag.
Note: This means that the trunk has the latest, possibly unstable code.
--Mike
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From: Michael S. <msa...@pc...> - 2005-06-23 16:29:52
|
All, We're pleased to announce the release of GUS 3.5, which is now available on the GUS Website at http://www.gusdb.org. The 3.5 release includes the introduction of proteomics support to the schema, PostgreSQL database compatibility, improved documentation, and significant additional schema and application layer fixes and enhancements. The 3.5 application framework is only compatible with the 3.5 schema, and vice versa. We hope to provide detailed upgrade instructions for existing instances in the next few weeks. Thanks, The GUS Development Community === Have you registered yet for the GUS 3.5 Workshop? For more information, including the Workshop agenda, please see: http://www.gusdb.org/workshop/ |
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From: Michael S. <msa...@pc...> - 2005-06-20 21:12:38
|
All, The GUS workshop agenda is now available on the GUS Workshop website: http://gusdb.org/workshop/agenda.php We'll be adding full abstracts shortly. If you have not yet registered, please take a minute to do so now: http://gusdb.org/workshop/registration.php Please let me know if you have any questions, comments, etc. Thanks, Mike |
|
From: Michael S. <msa...@pc...> - 2005-06-17 18:14:01
|
Hi Thomas, Yes, the cvs conversion mangled binary files. You should remove them through subversion (do a svn rm filename) and then readd them. You can either redownload them, or add them from an old working directory. Sorry for the trouble... --Mike On 6/17/05 2:00 PM, "Y. Thomas Gan" <yg...@pc...> wrote: > Hi Mike, > Here is a list of jar files that seem to be corrupted in svn. I can not > jar -tf on them. > Other jar files under WDK are fine. Can you fix them or do I have to > download them again? > > WDK/Controller/lib/java/struts-1.1.jar > WDK/View/lib/java/pager-taglib.jar > WDK/View/lib/java/wraptag.jar > WDK/View/lib/java/jstl.jar > WDK/View/lib/java/servlet-api-2.4.jar > WDK/View/lib/java/jsp-api-2.0.jar > WDK/View/lib/java/standard.jar > > -Thomas > >> -----Original Message----- >> From: gus...@li... >> [mailto:gus...@li...] On Behalf >> Of Michael Saffitz >> Sent: Friday, June 10, 2005 2:09 PM >> To: Aaron J. Mackey >> Cc: Gusdev gusdev-gusdev >> Subject: Re: [GUSDEV] Subversion Issue >> >> >> >> >> No, it looks like it may have been an end of line conversion >> issue. There are some additional options to address this in >> the conversion utility. For future switches I'll explore the >> trade-offs of using that. >> >> Fortunately there aren't too many binary files floating >> around the repository, so this is a relatively minor issue. >> >> --Mike >> >> >> On 6/10/05 2:58 PM, "Aaron J. Mackey" <am...@pc...> wrote: >> >>> Did you do CVS keyword substitution during the CVS export? >> If so, you >>> mangled any binary file that happened to have a >> keyword-like "string" >>> in it. >>> >>> -Aaron >>> >>> On Jun 10, 2005, at 2:52 PM, Michael Saffitz wrote: >>> >>>> >>>> Folks, >>>> >>>> We have our first subversion switch issue. It looks like binary >>>> files (i.e. >>>> jars) did not get properly handled in the move. I'm >> addressing them >>>> as I get errors, which can be strange: >>>> >>>> [javac] An exception has occurred in the compiler (1.4.2_04). >>>> Please file a bug at the Java Developer Connection >>>> (http://java.sun.com/cgi-bin/bugreport.cgi) after checking the Bug >>>> Parade >>>> for duplicates. Include your program and the following diagnostic >>>> in your >>>> report. Thank you. >>>> [javac] java.lang.InternalError: jzentry == 0, >>>> [javac] jzfile = -1502537536, >>>> [javac] total = 103, >>>> [javac] name = >> /home/msaffitz/pggus/gus/lib/java/pg74jdbc3.jar, >>>> [javac] i = 1, >>>> [javac] message = invalid LOC header (bad signature) >>>> [javac] at >> java.util.zip.ZipFile$2.nextElement(ZipFile.java: >>>> 321) >>>> [javac] at >>>> com.sun.tools.javac.v8.code.ClassReader.openArchive >>>> (ClassReader.java:975) >>>> [javac] at >>>> com.sun.tools.javac.v8.code.ClassReader.list(ClassReader.java:1218) >>>> [javac] at >>>> >> com.sun.tools.javac.v8.code.ClassReader.listAll(ClassReader.java:1339) >>>> [javac] at >>>> >> com.sun.tools.javac.v8.code.ClassReader.fillIn(ClassReader.java:1361) >>>> [javac] at >>>> com.sun.tools.javac.v8.code.ClassReader.complete(ClassReader.java: >>>> 1052) >>>> [javac] at >>>> com.sun.tools.javac.v8.code.Symbol.complete(Symbol.java:372) >>>> [javac] at >>>> com.sun.tools.javac.v8.comp.Enter.visitTopLevel(Enter.java:467) >>>> [javac] at >>>> com.sun.tools.javac.v8.tree.Tree$TopLevel.accept(Tree.java:390) >>>> [javac] at >>>> com.sun.tools.javac.v8.comp.Enter.classEnter(Enter.java:442) >>>> [javac] at >>>> com.sun.tools.javac.v8.comp.Enter.classEnter(Enter.java:456) >>>> [javac] at >>>> com.sun.tools.javac.v8.comp.Enter.complete(Enter.java:596) >>>> [javac] at com.sun.tools.javac.v8.comp.Enter.main >>>> (Enter.java:582) >>>> [javac] at >>>> com.sun.tools.javac.v8.JavaCompiler.compile(JavaCompiler.java:331) >>>> [javac] at >> com.sun.tools.javac.v8.Main.compile(Main.java:569) >>>> [javac] at com.sun.tools.javac.Main.compile(Main.java:36) >>>> [javac] at com.sun.tools.javac.Main.main(Main.java:27) >>>> >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------- >>>> This SF.Net email is sponsored by: NEC IT Guy Games. How >> far can you >>>> shotput a projector? How fast can you ride your desk chair >> down the >>>> office luge track? >>>> If you want to score the big prize, get to know the little guy. >>>> Play to win an NEC 61" plasma display: >> http://www.necitguy.com/?r=20 >>>> >> _______________________________________________ >>>> Gusdev-gusdev mailing list >>>> Gus...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>> >>> >>> -- >>> Aaron J. Mackey, Ph.D. >>> Project Manager, ApiDB Bioinformatics Resource Center >>> Penn Genomics Institute, University of Pennsylvania >>> email: am...@pc... >>> office: 215-898-1205 >>> fax: 215-746-6697 >>> postal: Penn Genomics Institute >>> Goddard Labs 212 >>> 415 S. University Avenue >>> Philadelphia, PA 19104-6017 >> >> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by: NEC IT Guy Games. How far >> can you shotput a projector? How fast can you ride your desk >> chair down the office luge track? If you want to score the >> big prize, get to know the little guy. >> Play to win an NEC 61" plasma display: >> http://www.necitguy.com/?r=20 >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Y. T. G. <yg...@pc...> - 2005-06-17 18:00:09
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Hi Mike, Here is a list of jar files that seem to be corrupted in svn. I can not jar -tf on them. Other jar files under WDK are fine. Can you fix them or do I have to download them again? WDK/Controller/lib/java/struts-1.1.jar WDK/View/lib/java/pager-taglib.jar WDK/View/lib/java/wraptag.jar WDK/View/lib/java/jstl.jar WDK/View/lib/java/servlet-api-2.4.jar WDK/View/lib/java/jsp-api-2.0.jar WDK/View/lib/java/standard.jar -Thomas > -----Original Message----- > From: gus...@li... > [mailto:gus...@li...] On Behalf > Of Michael Saffitz > Sent: Friday, June 10, 2005 2:09 PM > To: Aaron J. Mackey > Cc: Gusdev gusdev-gusdev > Subject: Re: [GUSDEV] Subversion Issue > > > > > No, it looks like it may have been an end of line conversion > issue. There are some additional options to address this in > the conversion utility. For future switches I'll explore the > trade-offs of using that. > > Fortunately there aren't too many binary files floating > around the repository, so this is a relatively minor issue. > > --Mike > > > On 6/10/05 2:58 PM, "Aaron J. Mackey" <am...@pc...> wrote: > > > Did you do CVS keyword substitution during the CVS export? > If so, you > > mangled any binary file that happened to have a > keyword-like "string" > > in it. > > > > -Aaron > > > > On Jun 10, 2005, at 2:52 PM, Michael Saffitz wrote: > > > >> > >> Folks, > >> > >> We have our first subversion switch issue. It looks like binary > >> files (i.e. > >> jars) did not get properly handled in the move. I'm > addressing them > >> as I get errors, which can be strange: > >> > >> [javac] An exception has occurred in the compiler (1.4.2_04). > >> Please file a bug at the Java Developer Connection > >> (http://java.sun.com/cgi-bin/bugreport.cgi) after checking the Bug > >> Parade > >> for duplicates. Include your program and the following diagnostic > >> in your > >> report. Thank you. > >> [javac] java.lang.InternalError: jzentry == 0, > >> [javac] jzfile = -1502537536, > >> [javac] total = 103, > >> [javac] name = > /home/msaffitz/pggus/gus/lib/java/pg74jdbc3.jar, > >> [javac] i = 1, > >> [javac] message = invalid LOC header (bad signature) > >> [javac] at > java.util.zip.ZipFile$2.nextElement(ZipFile.java: > >> 321) > >> [javac] at > >> com.sun.tools.javac.v8.code.ClassReader.openArchive > >> (ClassReader.java:975) > >> [javac] at > >> com.sun.tools.javac.v8.code.ClassReader.list(ClassReader.java:1218) > >> [javac] at > >> > com.sun.tools.javac.v8.code.ClassReader.listAll(ClassReader.java:1339) > >> [javac] at > >> > com.sun.tools.javac.v8.code.ClassReader.fillIn(ClassReader.java:1361) > >> [javac] at > >> com.sun.tools.javac.v8.code.ClassReader.complete(ClassReader.java: > >> 1052) > >> [javac] at > >> com.sun.tools.javac.v8.code.Symbol.complete(Symbol.java:372) > >> [javac] at > >> com.sun.tools.javac.v8.comp.Enter.visitTopLevel(Enter.java:467) > >> [javac] at > >> com.sun.tools.javac.v8.tree.Tree$TopLevel.accept(Tree.java:390) > >> [javac] at > >> com.sun.tools.javac.v8.comp.Enter.classEnter(Enter.java:442) > >> [javac] at > >> com.sun.tools.javac.v8.comp.Enter.classEnter(Enter.java:456) > >> [javac] at > >> com.sun.tools.javac.v8.comp.Enter.complete(Enter.java:596) > >> [javac] at com.sun.tools.javac.v8.comp.Enter.main > >> (Enter.java:582) > >> [javac] at > >> com.sun.tools.javac.v8.JavaCompiler.compile(JavaCompiler.java:331) > >> [javac] at > com.sun.tools.javac.v8.Main.compile(Main.java:569) > >> [javac] at com.sun.tools.javac.Main.compile(Main.java:36) > >> [javac] at com.sun.tools.javac.Main.main(Main.java:27) > >> > >> > >> > >> > >> > >> ------------------------------------------------------- > >> This SF.Net email is sponsored by: NEC IT Guy Games. How > far can you > >> shotput a projector? How fast can you ride your desk chair > down the > >> office luge track? > >> If you want to score the big prize, get to know the little guy. > >> Play to win an NEC 61" plasma display: > http://www.necitguy.com/?r=20 > >> > _______________________________________________ > >> Gusdev-gusdev mailing list > >> Gus...@li... > >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > >> > > > > -- > > Aaron J. Mackey, Ph.D. > > Project Manager, ApiDB Bioinformatics Resource Center > > Penn Genomics Institute, University of Pennsylvania > > email: am...@pc... > > office: 215-898-1205 > > fax: 215-746-6697 > > postal: Penn Genomics Institute > > Goddard Labs 212 > > 415 S. University Avenue > > Philadelphia, PA 19104-6017 > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: NEC IT Guy Games. How far > can you shotput a projector? How fast can you ride your desk > chair down the office luge track? If you want to score the > big prize, get to know the little guy. > Play to win an NEC 61" plasma display: > http://www.necitguy.com/?r=20 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Michael S. <msa...@pc...> - 2005-06-17 17:28:11
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All, This is a reminder to register for the GUS workshop if you haven't yet done so. We're trying to get an accurate count for the workshop, so please register even if we already know you're coming and/or you've requested to speak. You may register at: http://www.gusdb.org/workshop/registration.php A few additional notes: * The agenda will be published early next week. * We are making arrangements to webcast the conference for those not able to attend. If you're interested in participating through the webcast, please register using the URL above and note that you'll be remotely participating in the dietary restrictions box. * There are three recommended hotels for the conference: * PennTower: http://www.upenn.edu/penntower/ * Sheraton Univ. City: http://www.philadelphiasheraton.com/ * The Hilton Inn at Penn: http://www.theinnatpenn.com/ These three hotels are within walking distance. Other hotels in Center City, Philadelphia are accessible via public transportation and/or cabs (about a $5-15 fare depending on location). Note: There are many events occurring in Philadelphia the weekend of the 4th, and reserving a hotel room as soon as possible is highly recommended. Please let me know if you have any questions, Mike |
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From: Michael S. <msa...@pc...> - 2005-06-16 21:26:58
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Please see my earlier email for details. The most important thing to remember: if there's a small "gotcha" or caveat, it's going to totally befuddle someone new to GUS. Our postgres test database is ready as well, please see me for access. Also, remember that you'll need to update your $GUS_CONFIG_FILE's dbi settings when switching between plugdev and the postgres test database. --Mike |
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From: Michael S. <msa...@pc...> - 2005-06-16 20:50:53
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The repository clean up work is now done:
* pre-3.5 tags are the old trunk for 3.0 bug fixes
* the new trunk is 3.5 based for new (not 3.5) features
* the testing-3.5 is our candidate for release and for 3.5 bug fixes
plugdev has been wiped and is being readied for testing. Please see my
previous email about the various guidelines and practices. I'll send out
details about working with postgres shortly.
Please let me know if you have any questions.
Thanks,
Mike
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From: Steve F. <sfi...@pc...> - 2005-06-16 20:13:21
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folks- in svn, unlike cvs, when you have resolved the conflicts in a file you must tell svn that: svn resolve myfile.java steve |
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From: Steve F. <sfi...@pc...> - 2005-06-16 19:37:49
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yes, and both the uncommented lines must have no leading white space steve Jonathan Schug wrote: > I also had to uncomment this line: > > [miscellany] > > which is located 10-20 lines above the 'enable-auto-props = yes' line. > > Jonathan > > > Jonathan Schug - js...@pc... > > > On Jun 16, 2005, at 10:18 AM, Michael Saffitz wrote: > >> >> All, >> >> An important note about using subversion-- For newly added files to the >> repository, it will not automatically perform substitutions on >> keywords such >> as $Id$ or $Revision$. There are two ways to resolve this. >> >> On a file by file basis: >> >> svn propset svn:keywords "Id Revision" Filename >> >> This will tell subversion to substitute Id and Revision for Filename. >> >> If you want this by default (and I suggest you do!) than you can set >> it in >> your subversion config: >> >> emacs $HOME/.subversion/config >> >> uncomment # enable-auto-props = yes >> >> You may also wish to set an editor in this file (editor-cmd) if you >> have >> been getting errors about that. >> >> You'll need to update this file on every machine that you checkout from >> subversion from. (If you just use hera, zeus, and you're local linux >> desktop, then you only need to do this on one of those). >> >> Please let me know if you have any questions or difficulties setting >> this. >> My apologies that this isn't something I can do server-side-- "it's a >> feature, not a bug!" >> >> --Mike >> >> |
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From: Jonathan S. <js...@pc...> - 2005-06-16 19:24:44
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I also had to uncomment this line: [miscellany] which is located 10-20 lines above the 'enable-auto-props = yes' line. Jonathan Jonathan Schug - js...@pc... On Jun 16, 2005, at 10:18 AM, Michael Saffitz wrote: > > All, > > An important note about using subversion-- For newly added files to > the > repository, it will not automatically perform substitutions on > keywords such > as $Id$ or $Revision$. There are two ways to resolve this. > > On a file by file basis: > > svn propset svn:keywords "Id Revision" Filename > > This will tell subversion to substitute Id and Revision for Filename. > > If you want this by default (and I suggest you do!) than you can > set it in > your subversion config: > > emacs $HOME/.subversion/config > > uncomment # enable-auto-props = yes > > You may also wish to set an editor in this file (editor-cmd) if you > have > been getting errors about that. > > You'll need to update this file on every machine that you checkout > from > subversion from. (If you just use hera, zeus, and you're local linux > desktop, then you only need to do this on one of those). > > Please let me know if you have any questions or difficulties > setting this. > My apologies that this isn't something I can do server-side-- "it's a > feature, not a bug!" > > --Mike > > |
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From: Michael S. <msa...@pc...> - 2005-06-16 19:20:52
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This is an overview of the cleanup that will be occurring in the repository this afternoon at 4pm. Please remember to commit all changes to GUS and install before then. 1) The trunk for both GUS and install will be tagged as pre-3.5. 2) The 3.5 branches will be merged into the trunk. 3) The rel_3_5 branches will be removed. 4) Both projects will get testing-3.5 branches. Once complete, you'll need to do the following (for both GUS and install). For 3.0 codebases: From the project directory (i.e. $PROJECT_HOME/GUS or $PROJECT_HOME/install) svn switch https://www.cbil.upenn.edu/svn/gus/PROJECT/tags/pre-3.5 (replace PROJECT with GUS or install as appropriate). NOTE: You should not perform any commits against anything in the tags directory!! Commits should only be performed against the trunks or branches. Please see me for further details about fixing bugs in the 3.0 codebase. For 3.5 codebases From the project directory (i.e. $PROJECT_HOME/GUS or $PROJECT_HOME/install) svn switch https://www.cbil.upenn.edu/svn/gus/PROJECT/branches/testing-3.5 (replace PROJECT with GUS or install as appropriate). NOTE: only 3.5 bug fixes should be committed against the testing-3.5 branch. If you have a great new feature you want to begin implementing, you should checkout the trunk (after the move) and do your work there. Once testing is complete, the current revision on the testing-3.5 branch will be packaged and made into a tar.gz file for release. That revision will also be tagged (as release-3.5) and the testing-3.5 branch will be removed. Please let me know if you have any questions, Mike |
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From: Michael S. <msa...@pc...> - 2005-06-16 18:11:21
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Once 3.5 is frozen and the repository changes have been made, (i.e. Starting tomorrow morning), we'll be ready to conduct final testing. All Supported plugins will need to be tested in Oracle and Postgres. This should indirectly give the object layer a thorough testing as well. The plugdev Oracle database will be wiped clean this evening and available for testing, as will "gus", a Postgres database on hera. Please let me know if you need access to these. When testing plugins, the following general parameters should be followed: * No data should be loaded into the database except through the use of a Supported plugin. Supported plugins should not rely on data being loaded with a Community plugin. * No plugin should rely on software (including CPAN modules) that is not included in the GUS distribution _or_ that is not documented in the installation documents. At present, that is limited to: DBI, Parse::Yapp, XML::Simple, XML::Parser, XML::SAX. * Plugins should conform to the plugin development standards, especially in areas visible to the end-user (i.e. Command line arguments or documentation) * All plugins should be tested in commit mode. * Plugins may be tested against a subset of a datafile for time issues, but this subset should be representative of the datafile. (i.e. the subset should contain at least one record from the datafile in each format represented by the datafile). * All bugs/issues should be entered in the tracker unless they are immediately fixed. As gus_commit emails are sent, you should make sure your working copy of the repository stays updated by doing a svn update. To track our progress testing plugins, I propose that we use subversions properties system. Thus, when you have finished testing a plugin and are satisfied with the results, you should do: svn propset tested 'true' plugin_name.pm (replace plugin_name with the name of your plugin. This example assumes you're in the plugin directory- otherwise use the full path). You must commit after using propset. Please let me know if you have any comments or suggestions. --Mike |
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From: Angel P. <an...@ma...> - 2005-06-16 16:36:21
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Elisabetta Manduchi wrote: > > I'm pretty sure that this was brought up twice at recent CBIL meetings > (either the CBIL GUS meeting or the CBIL RAD one) and it was decided > that the tables should not be merged. However at the moment I do not > recall what motivated that decision. Does any cbilian remember? > Elisabetta > It was decided to keep them separate for practical query reasons. Table partitioning may aleviate this concern, but that has gonew nowhere as of yet. Also the schema for 3.5 is frozen. Period. Maybe 4.0, but I still think the practical reason to not merge outweighs the asthetic one to do so. -angel > --- > > On Thu, 16 Jun 2005, Steve Fischer wrote: > >> both RAD and DoTS have a ProjectLink tables with the exact same columns. >> >> in 3.5 we will combine this into one table in core. >> >> any objections? >> >> steve >> >> >> ------------------------------------------------------- >> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies >> from IBM. Find simple to follow Roadmaps, straightforward articles, >> informative Webcasts and more! Get everything you need to get up to >> speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Michael S. <msa...@pc...> - 2005-06-16 16:33:42
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Sorry for the confusion-- I filed the original bug on this, but this change WILL NOT occur in 3.5-- this is mostly a footnote to remember to revisit the issue for a future release. -- Mike On 6/16/05 12:23 PM, "Elisabetta Manduchi" <man...@pc...> wrote: > > I'm pretty sure that this was brought up twice at recent CBIL meetings > (either the CBIL GUS meeting or the CBIL RAD one) and it was decided that > the tables should not be merged. However at the moment I do not recall > what motivated that decision. Does any cbilian remember? > Elisabetta > > --- > > On Thu, 16 Jun 2005, Steve Fischer wrote: > >> both RAD and DoTS have a ProjectLink tables with the exact same columns. >> >> in 3.5 we will combine this into one table in core. >> >> any objections? >> >> steve >> >> >> ------------------------------------------------------- >> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies >> from IBM. Find simple to follow Roadmaps, straightforward articles, >> informative Webcasts and more! Get everything you need to get up to >> speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Michael S. <msa...@pc...> - 2005-06-16 16:32:47
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All, 3.5 is rapidly nearing release. At 4pm today it will be declared code complete and frozen (with one exception for the LoadOntologyEntry plugin). From 4pm to 5pm I'll be cleaning up the GUS repository to prepare for the release process. *** PLEASE make sure that you have committed all changes to the repositories prior to 4pm. This applies to the trunk (3.0 codebase) and the 3.5 branches, and applies to both the GUS and install projects. I'll send out further details about how to get and work with the 3.0 codebase and/or the 3.5 codebase after the cleanup. Both cases should be fairly trivial, but it does require this initial coordination for commits. After this change, things should slow down fairly significantly in the repository-- thanks for bearing with us as 3.5 is released. Thanks, Mike |
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From: Elisabetta M. <man...@pc...> - 2005-06-16 16:23:56
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I'm pretty sure that this was brought up twice at recent CBIL meetings (either the CBIL GUS meeting or the CBIL RAD one) and it was decided that the tables should not be merged. However at the moment I do not recall what motivated that decision. Does any cbilian remember? Elisabetta --- On Thu, 16 Jun 2005, Steve Fischer wrote: > both RAD and DoTS have a ProjectLink tables with the exact same columns. > > in 3.5 we will combine this into one table in core. > > any objections? > > steve > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Steve F. <sfi...@pc...> - 2005-06-16 16:15:22
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both RAD and DoTS have a ProjectLink tables with the exact same columns. in 3.5 we will combine this into one table in core. any objections? steve |
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From: Elisabetta M. <man...@pc...> - 2005-06-16 14:39:31
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Looks like you also have to uncomment the relevant section headers, e.g. [helpers] for the editor-cmd, etc. E. --- On Thu, 16 Jun 2005, Michael Saffitz wrote: > > All, > > An important note about using subversion-- For newly added files to the > repository, it will not automatically perform substitutions on keywords such > as $Id$ or $Revision$. There are two ways to resolve this. > > On a file by file basis: > > svn propset svn:keywords "Id Revision" Filename > > This will tell subversion to substitute Id and Revision for Filename. > > If you want this by default (and I suggest you do!) than you can set it in > your subversion config: > > emacs $HOME/.subversion/config > > uncomment # enable-auto-props = yes > > You may also wish to set an editor in this file (editor-cmd) if you have > been getting errors about that. > > You'll need to update this file on every machine that you checkout from > subversion from. (If you just use hera, zeus, and you're local linux > desktop, then you only need to do this on one of those). > > Please let me know if you have any questions or difficulties setting this. > My apologies that this isn't something I can do server-side-- "it's a > feature, not a bug!" > > --Mike > > |
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From: Michael S. <msa...@pc...> - 2005-06-16 14:18:34
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All, An important note about using subversion-- For newly added files to the repository, it will not automatically perform substitutions on keywords such as $Id$ or $Revision$. There are two ways to resolve this. On a file by file basis: svn propset svn:keywords "Id Revision" Filename This will tell subversion to substitute Id and Revision for Filename. If you want this by default (and I suggest you do!) than you can set it in your subversion config: emacs $HOME/.subversion/config uncomment # enable-auto-props = yes You may also wish to set an editor in this file (editor-cmd) if you have been getting errors about that. You'll need to update this file on every machine that you checkout from subversion from. (If you just use hera, zeus, and you're local linux desktop, then you only need to do this on one of those). Please let me know if you have any questions or difficulties setting this. My apologies that this isn't something I can do server-side-- "it's a feature, not a bug!" --Mike |
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