Error stack when executing admin.pl

[Ruth]

Hi,
When I run admin.pl I get the following stack, it executes fine but I
would like to fix the issue if possible. Is there a setting that I
need to change to set the pathway commons log file or an environment
variable that I am missing?

Thanks,
Ruth

log4j:ERROR setFile(null,true) call failed.
java.io.FileNotFoundException: /srv/www/tomcat5/base/logs/pc_log.txt
(No such file or directory)
at java.io.FileOutputStream.openAppend(Native Method)
at java.io.FileOutputStream.<init>(FileOutputStream.java:177)
at java.io.FileOutputStream.<init>(FileOutputStream.java:102)
at org.apache.log4j.FileAppender.setFile(FileAppender.java:
272)
at org.apache.log4j.FileAppender.activateOptions
(FileAppender.java:151)
at org.apache.log4j.DailyRollingFileAppender.activateOptions
(DailyRollingFileAppender.java:206)
at org.apache.log4j.config.PropertySetter.activate
(PropertySetter.java:247)
at org.apache.log4j.config.PropertySetter.setProperties
(PropertySetter.java:123)
at org.apache.log4j.config.PropertySetter.setProperties
(PropertySetter.java:87)
at org.apache.log4j.PropertyConfigurator.parseAppender
(PropertyConfigurator.java:645)
at org.apache.log4j.PropertyConfigurator.parseCategory
(PropertyConfigurator.java:603)
at org.apache.log4j.PropertyConfigurator.configureRootCategory
(PropertyConfigurator.java:500)
at org.apache.log4j.PropertyConfigurator.doConfigure
(PropertyConfigurator.java:406)
at org.apache.log4j.PropertyConfigurator.doConfigure
(PropertyConfigurator.java:432)
at org.apache.log4j.helpers.OptionConverter.selectAndConfigure
(OptionConverter.java:460)
at org.apache.log4j.LogManager.<clinit>(LogManager.java:113)
at org.apache.log4j.Logger.getLogger(Logger.java:85)
at org.apache.commons.logging.impl.Log4JLogger.getLogger
(Log4JLogger.java:229)
at org.apache.commons.logging.impl.Log4JLogger.<init>
(Log4JLogger.java:65)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0
(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance
(NativeConstructorAccessorImpl.java:39)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance
(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:
513)
at org.apache.commons.logging.impl.LogFactoryImpl.newInstance
(LogFactoryImpl.java:529)
at org.apache.commons.logging.impl.LogFactoryImpl.getInstance
(LogFactoryImpl.java:235)
at org.apache.commons.logging.LogFactory.getLog
(LogFactory.java:370)
at net.sf.ehcache.CacheManager.<clinit>(CacheManager.java:93)
at org.mskcc.pathdb.util.cache.EhCache.initCache(EhCache.java:
80)
at org.mskcc.pathdb.tool.Admin.main(Admin.java:97)
log4j:ERROR Either File or DatePattern options are not set for
appender [A1].

[Ethan Cerami]

Ruth:

To fix this, you need to update build.properties:

log4j.file= XXX

Ethan

--
Ethan Cerami
Computational Biology Center
Memorial Sloan-Kettering Cancer Center
http://cbio.mskcc.org