Loci.formats.in.SlideBook6Reader

Hi,

I have a pipeline running well on Linux which have Cellprofiler installed using yum package installation you have provided: http://cellprofiler.org/linux.html

Then we have installed a version of cellprofiler on our cluster, since it is not possible to install precompiled binary on our cluster, we built a version from the source. When I run the same pipleline, I got many errors as:

CP-JAVA 21:30:36.317 [Thread-0] ERROR loci.formats.ClassList - “loci.formats.in.SlideBook6Reader” is not valid.
CP-JAVA 21:30:36.483 [Thread-0] ERROR loci.formats.ClassList - “loci.formats.in.SlideBook6Reader” is not valid.

However, the process is still running and is outputting results. My question is: are these errors caused by running same pipleline on different version of Cellprofiler? Does it have any real impact on generating correct results?

Thanks,

My understanding is that these just have to do with different dependencies of these and older versions, which are evolving as we update and refine CP, and that as long as your pipeline is running it’s fine to ignore them.

Good to know. Thanks.

There are more, do you think that the same cause and shouldn’t impact on the results.

Thanks,

Xiaorong

Warning: org.apache.xerces.parsers.SAXParser: Property ‘http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit’ is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property ‘http://javax.xml.XMLConstants/property/accessExternalDTD’ is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property ‘http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit’ is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property ‘http://javax.xml.XMLConstants/property/accessExternalDTD’ is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property ‘http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit’ is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property ‘http://javax.xml.XMLConstants/property/accessExternalDTD’ is not recognized.
Warning: org.apache.xerces.parsers.SAXParser: Property ‘http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit’ is not recognized.
Thu May 12 03:51:55 2016: Image # 3455, module SaveImages # 16: 0.06 sec
Thu May 12 03:51:55 2016: Image # 3455, module ExportToSpreadsheet # 17: 0.00 sec
Exception in thread “Thread-0” java.lang.NullPointerException
Caught exception in class loci.formats.in.ZeissLMSReader.isThisType
Exception in thread “Thread-0” java.lang.NullPointerException
Caught exception in class loci.formats.in.ZeissLMSReader.isThisType
Exception in thread “Thread-0” java.lang.NullPointerException
Caught exception in class loci.formats.in.ZeissLMSReader.isThisType
Exception in thread “Thread-0” java.lang.NullPointerException
Caught exception in class loci.formats.in.ZeissLMSReader.isThisType
Exception in thread “Thread-0” java.lang.NullPointerException
Caught exception in class loci.formats.in.ZeissLMSReader.isThisType

That is my understanding, yes- as long as it’s running, these errors should not affect the output.