Re: [base] BASE2 + Solaris crashes recommended JVM
* System specs Solaris 10 / SPARC, 6 GB, in a zone JDK 1.5.0_01 MySQL 4.1.18 Tomcat 5.5 * Problem 1: using binary BASE 2.0 When running the 'updatedb.sh' script, java crashes after building the initial database: [0%]Building database [30%] Database built successfully. java.lang.NullPointerException at net.sf.basedb.core.Update.getSchemaVersion(Update.java:319) at net.sf.basedb.core.Update.adjustExistingItems(Update.java:599) at net.sf.basedb.install.InitDB.main(InitDB.java:66) I have checked the code and it turns out that it is currently not possible to update the RC1 release. The schemaVersion stuff that is triggering the NullPointerException was added after the RC1 release to make it easier to upgrade! If you have important data maybe we can fix this for the 2.0.1 release. Thanks for the quick reply! So, no pressing need to fix this, we were just taking the shortest route towards testing 2.0 (+ the initialization wasn't working, see below). Populating a new database with 'initdb.sh' runs into similar problems: [0%]Building database. [30%] Database built successfully. [35%] Initialising database... java.lang.NullPointerException at net.sf.basedb.core.HibernateUtil.close(HibernateUtil.java:881) at net.sf.basedb.core.Install.initDatabase(Install.java:605) at net.sf.basedb.install.InitDB.main(InitDB.java:67) Are you really using the released 2.0 binary here? The reason that I ask is that we found the same problem in the trunk of our subversion server this morning. But that code was only a couple of days old. We don't get the error with the released 2.0 binary. I would assume so, plus we get the same behaviour with the source distribution. We downloaded the Aug 31 release of base-2.0.tar.gz for the binary and base-2.0-src.tar.gz for the self-compiled version, and both yield the same error message, even when using the latest Java (se Problem 3). I'd show you the output from More about this server but it throws an exception too (db version mismatch perhaps): 10:50:16,385 ERROR [jsp]:704 - Servlet.service() for servlet jsp threw exception java.lang.NullPointerException at net.sf.basedb.core.Application.getSchemaVersion(Application.java:202) The link used was http://www.thep.lu.se/~jari/base/base-2.0.tar.gz So basically, we're stuck - is there anything else we can do to help you figue out what is going wrong? The only things I can think of are: A) routines called subsequently by net.sf.basedb.install.InitDB are not picking up the new Java installation - if that would even be an issue? B) there's a mySQL version problem (since it's HibernateUtil that's complaining). * Problem 2: compiling BASE 2.0 Base 2.0 does build successfully from source but with LOTS of warnings using Java 1.5.0_01, but no change from the above situation. Excerpt: [javac] /install/source/base-2.0-src/src/core/net/sf/basedb/core/ HibernateUtil.java:1425: warning: [unchecked] unchecked conversion [javac] found : java.util.Iterator [javac] required: java.util.Iteratororg.hibernate.mapping.PersistentClass [javac] return cfg.getClassMappings(); [javac]^ [javac] /install/source/base-2.0-src/src/core/net/sf/basedb/core/ HibernateUtil.java:1553: warning: [unchecked] unchecked cast [javac] found : java.util.Iterator [javac] required: java.util.Iteratororg.hibernate.mapping.Table [javac] IteratorTable tables = (IteratorTable)cfg.getTableMappings(); [javac] ^ This is a problem with the older java compiler which just ignore our diretions not to generate warnings. The problem was fixed in a later version. I don't remember if it was 1.5.0_04 or some other version. OK, good to know. Maybe something for the installation page? We'll stick with 1.5.0_08 then - if we can get the initdb.sh script to work, that is! Regards, /Emil * Problem 3: using BASE 2.0 w/ JDK 1.5.0_08 Suspecting a major java problem, we tried installing a local version of the latest JDK (1.5.0_08) and repeating the above. Compiling is now OK, and using binary or source makes no difference. However, when trying either 'updatedb.sh' or 'initdb.sh', we get the exact same behaviour as before (NullPointerException). Note: BASE 2 itself (the tomcat / web service part) works as far as logging in, but afaik needs to be updated/reinitialized to support the new features of 2.0. Yes, you must run the update. /Nicklas - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
Re: [base] BASE2 + Solaris crashes recommended JVM
I am not able to reproduce the error. Unfortunately there is a glitch in the error handling which causes a second error to hide the original one. If you turn on debugging there might be some more information displayed. You turn on debugging by editing the /www/WEB-INF/classes/log4j.properties file. In the Base 2 CORE loggers section change the line: log4j.logger.net.sf.basedb.core=warn to: log4j.logger.net.sf.basedb.core=debug and run the initdb.sh script again. /Nicklas Emil Lundberg wrote: * System specs Solaris 10 / SPARC, 6 GB, in a zone JDK 1.5.0_01 MySQL 4.1.18 Tomcat 5.5 * Problem 1: using binary BASE 2.0 When running the 'updatedb.sh' script, java crashes after building the initial database: [0%]Building database [30%] Database built successfully. java.lang.NullPointerException at net.sf.basedb.core.Update.getSchemaVersion(Update.java:319) at net.sf.basedb.core.Update.adjustExistingItems(Update.java:599) at net.sf.basedb.install.InitDB.main(InitDB.java:66) I have checked the code and it turns out that it is currently not possible to update the RC1 release. The schemaVersion stuff that is triggering the NullPointerException was added after the RC1 release to make it easier to upgrade! If you have important data maybe we can fix this for the 2.0.1 release. Thanks for the quick reply! So, no pressing need to fix this, we were just taking the shortest route towards testing 2.0 (+ the initialization wasn't working, see below). Populating a new database with 'initdb.sh' runs into similar problems: [0%]Building database. [30%] Database built successfully. [35%] Initialising database... java.lang.NullPointerException at net.sf.basedb.core.HibernateUtil.close(HibernateUtil.java:881) at net.sf.basedb.core.Install.initDatabase(Install.java:605) at net.sf.basedb.install.InitDB.main(InitDB.java:67) Are you really using the released 2.0 binary here? The reason that I ask is that we found the same problem in the trunk of our subversion server this morning. But that code was only a couple of days old. We don't get the error with the released 2.0 binary. I would assume so, plus we get the same behaviour with the source distribution. We downloaded the Aug 31 release of base-2.0.tar.gz for the binary and base-2.0-src.tar.gz for the self-compiled version, and both yield the same error message, even when using the latest Java (se Problem 3). I'd show you the output from More about this server but it throws an exception too (db version mismatch perhaps): 10:50:16,385 ERROR [jsp]:704 - Servlet.service() for servlet jsp threw exception java.lang.NullPointerException at net.sf.basedb.core.Application.getSchemaVersion(Application.java:202) The link used was http://www.thep.lu.se/~jari/base/base-2.0.tar.gz So basically, we're stuck - is there anything else we can do to help you figue out what is going wrong? The only things I can think of are: A) routines called subsequently by net.sf.basedb.install.InitDB are not picking up the new Java installation - if that would even be an issue? B) there's a mySQL version problem (since it's HibernateUtil that's complaining). * Problem 2: compiling BASE 2.0 Base 2.0 does build successfully from source but with LOTS of warnings using Java 1.5.0_01, but no change from the above situation. Excerpt: [javac] /install/source/base-2.0-src/src/core/net/sf/basedb/core/ HibernateUtil.java:1425: warning: [unchecked] unchecked conversion [javac] found : java.util.Iterator [javac] required: java.util.Iteratororg.hibernate.mapping.PersistentClass [javac] return cfg.getClassMappings(); [javac]^ [javac] /install/source/base-2.0-src/src/core/net/sf/basedb/core/ HibernateUtil.java:1553: warning: [unchecked] unchecked cast [javac] found : java.util.Iterator [javac] required: java.util.Iteratororg.hibernate.mapping.Table [javac] IteratorTable tables = (IteratorTable)cfg.getTableMappings(); [javac] ^ This is a problem with the older java compiler which just ignore our diretions not to generate warnings. The problem was fixed in a later version. I don't remember if it was 1.5.0_04 or some other version. OK, good to know. Maybe something for the installation page? We'll stick with 1.5.0_08 then - if we can get the initdb.sh script to work, that is! Regards, /Emil * Problem 3: using BASE 2.0 w/ JDK 1.5.0_08 Suspecting a major java problem, we tried installing a local version of the latest JDK (1.5.0_08) and repeating the above. Compiling is now OK, and using binary or source makes no difference. However, when trying either 'updatedb.sh' or 'initdb.sh', we get the exact same
[base] Users Manual for BASE 2?
Hello, Any idea when the User's Manual for BASE 2 will be available? We're looking for a microarray DB system, and I've gotten a trial account on the BASE 2 demo server, but it's hard to figure out how to get started on your own. Thanks, Jenny Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: [EMAIL PROTECTED] - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
