Difference between revisions of "Known Issues"

(geWorkbench 2.5.0)
(Gatekeeper stops files from running)
 
(78 intermediate revisions by the same user not shown)
Line 1: Line 1:
==geWorkbench 2.5.0==
+
==Installation - top issues==
* '''Workspace''' (#3577) - The "merge" function for expression datasets is not working.
+
===Windows platform (maybe also Linux)===
 +
The Windows installers will not run if a version of Java higher than Java 8 update 51 is installed on the machine.  For workarounds, see [[Download_and_Installation#IMPORTANT_Note_for_Windows_.28and_Linux.29|IMPORTANT Note for Windows (and_Linux)]].
  
==geWorkbench 2.4.1==
+
===Macintosh OSX platform===
'''BLAST''' - Due to a change in the output from the NCBI BLAST server, sequence alignments are not being displayed.  This will be fixed in version 2.5.0 by switching to using the XML results file.
+
====Gatekeeper stops files from running====
  
'''Marker Annotations''' - As of September 30th, 2013, NCI-CBIIT is expected to deactivate the caBIO service on which the geWorkbench Marker Annotation component dependsgeWorkbench 2.5.0 uses the bioDBNet service as its data source instead.
+
The first time a downloaded file (e.g. a command file) is run, you may need to tell Gatekeeper to allow it to runPlease see instructions at [[Download_and_Installation#IMPORTANT_note_for_MacOSX| IMPORTANT note for MacOSX]].
  
 +
==geWorkbench 2.6.0==
 +
In the CNKB component, interactome export is currently only enabled for three smaller interactomes:  BCi, HGi_Sun, and Geneways.  Export of larger interactomes is being implemented through server-side changes and will be enabled in a subsequent update.  However, export of larger interactomes directly into the Workspace is not recommended.
  
Issues for 2.4.1 are the same as for those listed for 2.4.0, except that the first BLAST issue, dealing with the HTML page parsing, has been fixed.
+
==geWorkbench 2.6.0 and prior==
 +
===Housekeeping Genes Normalizer and tab-delimited expression files===
 +
If a gene expression set is loaded into geWorkbench in tab-delimited format, the Housekeeping Genes Normalizer will not work. The workaround is to the save the data back to disk in the ".exp" format - to do this, right-click on the data node and select "Save".  Then load the data back in to geWorkbench as format type ".exp".  The Housekeeping Genes Normalizer can now be used.
  
'''BLAST''' - (also in previous versions) The NCBI BLAST server may occasionally return an error when sequences are searched from geWorkbench. The problem appears to depend on the load on the NCBI BLAST server. When multiple sequences are being submitted, geWorkbench submits them one-at-time to the BLAST server.  When many sequences are submitted, it may be more likely that such a server-side problem will be encountered at some point and the search cancelled.
+
===MarkUs===
 +
Viewing MarkUs results directly in geWorkbench is only available when a 32-bit version of Java is being used.  In all other cases, the MarkUs results can instead be opened in an external web browser. However, several steps, detailed in the [[MarkUs#Java_Requirements_for_Viewing_MarkUs_Results| MarkUs tutorial]], are necessary to set up the use of Java in the web browser.
  
==geWorkbench 2.4.0==
+
===Cytoscape===
The following problems have been noted in geWorkbench 2.4.0.  Some may apply to earlier releases as well.
+
When a gene network node is selected (left-click) within Cytoscape, and then right-clicked on, a detailed menu of annotation choices should appearHowever, if the node is in the right quarter of the display box, the gene menu instantly disappears and is replaced by the background right-click menu.  May occur in this and previous releases (Mantis issue #3194).  To get the menu, decrease the network size (zoom out), or move the network left.
* '''BLAST''' (9/26/2012) - due to a change in the HTML result format from the NCBI website, BLAST in geWorkbench 2.4.0 and all previous versions no longer works. 
 
* '''ARACNe2''' -  
 
** (#2885) ARACNe and MINDy, if local job cancellation is requested, call a non-safe method, thread.stop(), which can occasionally produce an exception.
 
* '''Java 7''' - geWorkbench 2.4.0 was developed and tested using the Java 6 JDK and JREAlthough several incompatibilites with Java 7 were identified and fixed, as least one remains, shown below.  For this reason, please only use Java 6 JREs when running geWorkbench 2.4.0 or earlier.
 
** '''Marker Annotations''' - (#3072) does not receive activated marker set, caBIO client library conflict with Java 7.
 
* '''BLAST''' - (#2825) the maximum number of hits returned is 50, even if more were requested.
 
* '''caArray''' - (#2893) due to a synchronization problem, a large empty white space may occasionally appear in the caArray list of experiments.
 
* '''Cytoscape'''
 
** (#2843) if an instance of Cytoscape is running on a machine, and then Cytoscape is also loaded in geWorkbench, you may see a warning "org.cytoscape.coreplugin.cpath2.http.HTTPServer[WARN]: HTTPServer couldn't create socket.".
 
** (#2716) Direct LinkOuts from the right-click menu to UniProt may not workHowever, they do work when selected from the Cytoscape Data Panel.
 
* '''GenePattern connectivity''' (#2701) - if you successfully connect to a GenePattern server, and later that server is no longer available, you will experience a time-out delayThis was seen when first connecting to a GP server through a firewall via VPN, then trying again without the VPN.
 
* '''GenomeSpace''' - transfer of large data files is not supported.  This has been fixed in development (Mantis issue #3273).
 
* '''Grid Services/Dispatcher Service''':
 
  
As of release 2.3.0, outbound data (from geWorkbench to the grid service) is moved using caTransfer, both from geWorkbench to the Dispatcher, and from the Dispatcher to the grid service. Returning data is transferred for both hops as a base-64 encoded string, which for very large data sets can lead to an out-of-memory error. Full replacement with caTransfer is being investigated.
+
Sometimes, the first time Cytoscape is used in geWorkbench, the lower parameter window covers the entire component, so that the network diagram is hidden.  It is hard to recognize this is what has happened, but the top of the panel can just be pulled down to reveal the network.
  
The error message will read:
+
===Use of incomplete annotation file causes errors in MRA-FET analysis===
 +
If an annotation file is loaded along with a microarray dataset, but the annotation file does not contain entries for all markers present in the dataset, then at least for the MRA-FET analysis, an incorrect result will be obtained.  Mantis issue #3839.
  
Out-of-memory error: Java heap space
+
===PCA and 64-bit Java===
It is advisable to restart geWorkbench.
+
The PCA 3D visualization does not currently work when using 64-bit Java, which is now the default on all platforms. It will work if a 32-bit version of Java is used to run geWorkbench (not available for Mac OS X).
You may also wish to increase the geWorkbench memory size.  
 
  
In this case, as the message states, it is advisable to restart geWorkbench. Instructions for increasing the amount of memory available to Java are available in the geWorkbench FAQ. For Java memory requests larger than about 1.5 GB, running geWorkbench using a 64-bit Java Runtime Environment (JRE) will be necessary.
+
===PCA and OpenGL version===
 +
The PCA 3D viewer requires that the computer display driver support OpenGL version 1.2 or higher. If it does not, a warning message will be displayed at the time the user attempts to create a 3D plot. Any recent graphics card should provide this support.
  
==Any current release==
+
===BLAST===
 +
(first reported in 2.4.1)
 +
The NCBI BLAST server may occasionally return an error when sequences are searched from geWorkbench. The problem appears to depend on the load on the NCBI BLAST server. When multiple sequences are being submitted, geWorkbench submits them one-at-time to the BLAST server.  When many sequences are submitted, it may be more likely that such a server-side problem will be encountered at some point and the search cancelled.
  
===64-bit Java issue===
+
===Running more than one copy of geWorkbench simultaneously===
Affects: GSEA, Markus, Pudge and PCA.
+
While running an analysis, some geWorkbench components write data to temporary files with non-unique names.  For this reason, two copies of geWorkbench should not be running at the same time, and especially not running the same analysis.
  
Several geWorkbench components make use of the embedded JDIC web browser.  The version of JDIC used in geWorkbench is not entirely compatible with 64-bit versions of Java.  If this problem is encountered, these components will instead transfer the display to your computer's default web browser.  However the displayed web page will not automatically update or interoperate with geWorkbench.
+
===Embedded browser not compatible with 64-bit Java===
 +
Affects: GSEA, MarkUs, Pudge.
  
===Mac-related issues===
+
Several geWorkbench components make use of a 32-bit embedded JDIC web browser.  This browser will not display when using 64-bit Java JREs (now the default for geWorkbench on all platforms). If this situation is encountered, these components will instead offer a link to display the results in your computer's default web browser. However the displayed web page will not automatically update or interoperate with geWorkbench.
====Java 7 on Mac====
 
This affects 10.7.3 and later versions of Mac OS X.
 
  
With a recent Java update, Apple has removed the Java plugin for all web browsersIf you load a web page which calls for this plugin, you will be prompted to download Java 7 from Oracle, which does support a browser pluginHowever, geWorkbench requires Java 6.   
+
===Astex viewer in MarkUs===
 +
====Windows====
 +
The MarkUs results display includes the Astex molecular structure viewer, which is a Java appletFor this to run, a JRE must be available which matches the architecture (32 or 64-bit) of the browser being usedFor Windows (as of early 2015), the default versions of Firefox and Chrome are 32-bit, so a 32-bit JRE must be installed on the computer to use this applet in the default browser versions.   
  
* The following links contain instructions for reverting to Java 6 after installing Java 7, should you so desire: [http://docs.oracle.com/javase/7/docs/webnotes/install/mac/mac-install-faq.html JDK 7 Installation for Mac OS X]
+
As of February 2015, Chrome is available in a 64-bit version for Windows as a special download, and Firefox is planning a March release of a 64-bit version.
  
* See also the [http://docs.oracle.com/javase/7/docs/webnotes/install/mac/mac-install-faq.html Mac OS X Platform Install FAQ]
+
====Getting Java====
 +
Particular versions of the Java JRE can be downloaded from http://java.oracle.com. 32-bit versions of the JRE include "x86" in their descriptions and "i586" in their file names. Additional information on configuring Java can be found on the [[MarkUs|MarkUs]] tutorial page.
  
* More details about Java 6 and 7 are also found here:  [http://docs.oracle.com/javase/7/docs/webnotes/install/mac/mac-preferences.html Note for Users of Macs that Include Apple Java 6]
+
===Cytoscape loading===
 +
Cytoscape is by default enabled in the [[Component_Configuration_Manager|CCM]].  This is to prevent certain problems that have been seen if it is loaded later, after geWorkbench has completed its startup.  If Cytoscape is unloaded and then later reloaded into the CCM, geWorkbench should be restarted. (c.f. Mantis issue #3381 and links to related issues therein).
  
* Not directly relevant to geWorkbench, but on the same topic: [http://support.apple.com/kb/HT5559?viewlocale=en_US Java for OS X 2012-006: How to re-enable the Apple-provided Java SE 6 applet plug-in and Web Start functionality]
+
===Mac-related issues===
  
 
====Building from source on Apple Mac OS X (tested in Lion 10.7)====
 
====Building from source on Apple Mac OS X (tested in Lion 10.7)====
Line 69: Line 68:
 
** Magic Mouse: In System Preferences, enable "Secondary click".
 
** Magic Mouse: In System Preferences, enable "Secondary click".
  
====PowerPC-based Macintosh computers====
+
====Cytoscape in 10.6.8====
Java 6 is not available for the PowerPC platform, regardless of the version of OS X. For this reason, recent versions of geWorkbench which require Java 6 will not run on PowerPC Macintosh computers.
+
On OSX 10.6.8, but not 10.7 or later, an extra window may pop up when a network is displayed in CytoscapeNo workaround is known.
 
 
===Installer Issues===
 
* We observed on a Windows 7 platform, that if geWorkbench, including the JRE6, is installed directly from a USB memory stick, the installation may silently fail.  The machine was running the current version of Norton Internet Security.  Copying the installer to the hard disk and installing from there solved the problem (Observed for geWorkbench 2.3.0).
 
* Versions of Norton Internet Security "Sonar" prior to NIS2011 may detect and delete a file generated during the installation process, "Install.exe"This will silently terminate the install.  If this occurs, disable the Sonar feature during installation, or disable your antivirus protection during the installation.
 
  
 
===Grid Issues===
 
===Grid Issues===
Line 89: Line 84:
 
These problems arise because the j3d libraries in the system java extension directory have higher priority than those in geworkbench.
 
These problems arise because the j3d libraries in the system java extension directory have higher priority than those in geworkbench.
  
By copying the appropriate j3d and jogl files into a directory with higher precedence, these problems can be avoided.  The following steps have been tested under Mac OS X 10.7 (Lion) but should work for earlier version also.
+
By copying the appropriate j3d and jogl files into a directory with higher precedence, these problems can be avoided.  The following steps have been tested under Mac OS X 10.7 (Lion) but should work for other versions also.
  
 
The safest method is to place the updated files within the user's own directory structure.  These changes will then apply only to that user and can be easily undone if needed.
 
The safest method is to place the updated files within the user's own directory structure.  These changes will then apply only to that user and can be easily undone if needed.
Line 100: Line 95:
 
   chflags hidden ~/Library
 
   chflags hidden ~/Library
  
* Copy the following java3d 1.5 libs from the geworkbench installation to the above java extensions directory:
+
* Copy the following java3d 1.5 libs from the geworkbench installation to the java extensions directory ~/Library/Java/Extensions:
 
**    geworkbench/lib/j3dcore.jar
 
**    geworkbench/lib/j3dcore.jar
 
**    geworkbench/lib/j3dutils.jar
 
**    geworkbench/lib/j3dutils.jar
 
**    geworkbench/lib/vecmath.jar
 
**    geworkbench/lib/vecmath.jar
  
* Next, download jogl libs from http://download.java.net/media/jogl/builds/archive/jsr-231-1.1.1/jogl-1.1.1-macosx-universal.zip, extract and copy the following files from the extracted lib directory to the your own user extensions directory ~/Library/Java/Extensions:
+
(Note - The java3d-1.5.1 files can also be downloaded from the [http://www.oracle.com/technetwork/java/javasebusiness/downloads/java-archive-downloads-java-client-419417.html#java3d-1.5.1-oth-JPR Oracle Java3D distribution site]).
 +
 
 +
* Next, [http://download.java.net/media/jogl/builds/archive/jsr-231-1.1.1/jogl-1.1.1-macosx-universal.zip download the jogl libs], then extract and copy the following files from the extracted lib directory to the your own user extensions directory ~/Library/Java/Extensions:
 
**    gluegen-rt.jar,
 
**    gluegen-rt.jar,
 
**    jogl.jar,
 
**    jogl.jar,

Latest revision as of 11:29, 22 December 2016

Installation - top issues

Windows platform (maybe also Linux)

The Windows installers will not run if a version of Java higher than Java 8 update 51 is installed on the machine. For workarounds, see IMPORTANT Note for Windows (and_Linux).

Macintosh OSX platform

Gatekeeper stops files from running

The first time a downloaded file (e.g. a command file) is run, you may need to tell Gatekeeper to allow it to run. Please see instructions at IMPORTANT note for MacOSX.

geWorkbench 2.6.0

In the CNKB component, interactome export is currently only enabled for three smaller interactomes: BCi, HGi_Sun, and Geneways. Export of larger interactomes is being implemented through server-side changes and will be enabled in a subsequent update. However, export of larger interactomes directly into the Workspace is not recommended.

geWorkbench 2.6.0 and prior

Housekeeping Genes Normalizer and tab-delimited expression files

If a gene expression set is loaded into geWorkbench in tab-delimited format, the Housekeeping Genes Normalizer will not work. The workaround is to the save the data back to disk in the ".exp" format - to do this, right-click on the data node and select "Save". Then load the data back in to geWorkbench as format type ".exp". The Housekeeping Genes Normalizer can now be used.

MarkUs

Viewing MarkUs results directly in geWorkbench is only available when a 32-bit version of Java is being used. In all other cases, the MarkUs results can instead be opened in an external web browser. However, several steps, detailed in the MarkUs tutorial, are necessary to set up the use of Java in the web browser.

Cytoscape

When a gene network node is selected (left-click) within Cytoscape, and then right-clicked on, a detailed menu of annotation choices should appear. However, if the node is in the right quarter of the display box, the gene menu instantly disappears and is replaced by the background right-click menu. May occur in this and previous releases (Mantis issue #3194). To get the menu, decrease the network size (zoom out), or move the network left.

Sometimes, the first time Cytoscape is used in geWorkbench, the lower parameter window covers the entire component, so that the network diagram is hidden. It is hard to recognize this is what has happened, but the top of the panel can just be pulled down to reveal the network.

Use of incomplete annotation file causes errors in MRA-FET analysis

If an annotation file is loaded along with a microarray dataset, but the annotation file does not contain entries for all markers present in the dataset, then at least for the MRA-FET analysis, an incorrect result will be obtained. Mantis issue #3839.

PCA and 64-bit Java

The PCA 3D visualization does not currently work when using 64-bit Java, which is now the default on all platforms. It will work if a 32-bit version of Java is used to run geWorkbench (not available for Mac OS X).

PCA and OpenGL version

The PCA 3D viewer requires that the computer display driver support OpenGL version 1.2 or higher. If it does not, a warning message will be displayed at the time the user attempts to create a 3D plot. Any recent graphics card should provide this support.

BLAST

(first reported in 2.4.1) The NCBI BLAST server may occasionally return an error when sequences are searched from geWorkbench. The problem appears to depend on the load on the NCBI BLAST server. When multiple sequences are being submitted, geWorkbench submits them one-at-time to the BLAST server. When many sequences are submitted, it may be more likely that such a server-side problem will be encountered at some point and the search cancelled.

Running more than one copy of geWorkbench simultaneously

While running an analysis, some geWorkbench components write data to temporary files with non-unique names. For this reason, two copies of geWorkbench should not be running at the same time, and especially not running the same analysis.

Embedded browser not compatible with 64-bit Java

Affects: GSEA, MarkUs, Pudge.

Several geWorkbench components make use of a 32-bit embedded JDIC web browser. This browser will not display when using 64-bit Java JREs (now the default for geWorkbench on all platforms). If this situation is encountered, these components will instead offer a link to display the results in your computer's default web browser. However the displayed web page will not automatically update or interoperate with geWorkbench.

Astex viewer in MarkUs

Windows

The MarkUs results display includes the Astex molecular structure viewer, which is a Java applet. For this to run, a JRE must be available which matches the architecture (32 or 64-bit) of the browser being used. For Windows (as of early 2015), the default versions of Firefox and Chrome are 32-bit, so a 32-bit JRE must be installed on the computer to use this applet in the default browser versions.

As of February 2015, Chrome is available in a 64-bit version for Windows as a special download, and Firefox is planning a March release of a 64-bit version.

Getting Java

Particular versions of the Java JRE can be downloaded from http://java.oracle.com. 32-bit versions of the JRE include "x86" in their descriptions and "i586" in their file names. Additional information on configuring Java can be found on the MarkUs tutorial page.

Cytoscape loading

Cytoscape is by default enabled in the CCM. This is to prevent certain problems that have been seen if it is loaded later, after geWorkbench has completed its startup. If Cytoscape is unloaded and then later reloaded into the CCM, geWorkbench should be restarted. (c.f. Mantis issue #3381 and links to related issues therein).

Mac-related issues

Building from source on Apple Mac OS X (tested in Lion 10.7)

There is an issue with the Java 3D library included with Mac OS X. In order to build geWorkbench from source, one must either install certain files from J3D 1.5, or delete the PCA component from the geWorkbench components directory (#2495).

  • To configure J3D on the Mac, please see the instructions below.
  • To just remove the PCA component, find the geWorkbench installation directory and follow this path: components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule. In the gpmodule directory, delete the folder "pca".

Mouse-button issues (tested in OS X 10.7 Lion )

  • Right-click contextual menu: On the Mac, control-click can substitute for the PC's "right-click" action, and bring up a contextual menu. However, this is not implemented in geWorkbench on the Mac. The following work-arounds are available:
    • Trackpad: In System Preferences, enable "Secondary click". You can choose 3 options on how this will work, including clicking in the lower-right-hand corner of the trackpad.
    • Magic Mouse: In System Preferences, enable "Secondary click".

Cytoscape in 10.6.8

On OSX 10.6.8, but not 10.7 or later, an extra window may pop up when a network is displayed in Cytoscape. No workaround is known.

Grid Issues

  • For grid services hosted inside the Columbia firewall, the service metadata cannot be retrieved from outside the firewall. Instead, generic metadata will be displayed. You may see a delay of up to 30 seconds while geWorkbench attempts to retrieve the service metadata, before a timeout occurs and the generic metadata is substituted.

Previous Releases

For issues with previous releases, please see the Previous Release Issues page.

Configuring J3D on the Mac for gpmodule PCA

The Java3D version included in geworkbench is 1.5. On the Mac platform, an earlier version (1.3) is installed in /System/Library/Java/Extensions/. Unless this is fixed on the user's Mac,

  1. geWorkbench cannot be built from source, as a compile error is generated, and
  2. PCA 3D plots cannot be used on the Mac when the Installer version is used.

These problems arise because the j3d libraries in the system java extension directory have higher priority than those in geworkbench.

By copying the appropriate j3d and jogl files into a directory with higher precedence, these problems can be avoided. The following steps have been tested under Mac OS X 10.7 (Lion) but should work for other versions also.

The safest method is to place the updated files within the user's own directory structure. These changes will then apply only to that user and can be easily undone if needed.

  • If the directory ~/Library/Java/Extensions does not exist, create it, where "~" refers to the User's home directory.
    • Note - in OS X 10.7 Lion, the ~/Library folder may be hidden by default. You can make it visible in the Finder by holding down the "option" key while selecting "Go" in the Finder menu.
    • Alternatively, to make the ~/Library folder always visible, execute the following command in a terminal window:
 chflags nohidden ~/Library/
 You can undo this with
 chflags hidden ~/Library
  • Copy the following java3d 1.5 libs from the geworkbench installation to the java extensions directory ~/Library/Java/Extensions:
    • geworkbench/lib/j3dcore.jar
    • geworkbench/lib/j3dutils.jar
    • geworkbench/lib/vecmath.jar

(Note - The java3d-1.5.1 files can also be downloaded from the Oracle Java3D distribution site).

  • Next, download the jogl libs, then extract and copy the following files from the extracted lib directory to the your own user extensions directory ~/Library/Java/Extensions:
    • gluegen-rt.jar,
    • jogl.jar,
    • libgluegen-rt.jnilib,
    • libjogl.jnilib,
    • libjogl_awt.jnilib,
    • libjogl_cg.jnilib

If you have system admin privileges on the machine, you can instead update the files for all users in /Library/Java/Extensions, however we do not recommend this.

General

  • Filtering a data set may after an analysis has already been run may invalidate objects that arose from the original, unfiltered dataset. Any filtering should be done before any analysis which creates child result nodes, e.g. a t-test, ANOVA etc.
  • Promoter panel (issue #1988) - under very particular conditions, where a letter has a score and height of zero, and where an external display is being used on a Macintosh computer, a graphics error can be reported to the console. However, this error does not cause any problems.