Known Issues - Revision history

Smith: /* Gatekeeper stops files from running */

2016-12-22T16:29:33Z

‎Gatekeeper stops files from running

Smith at 20:07, 4 November 2015

2015-11-04T20:07:19Z

Smith: /* Housekeeping Genes Normalizer and tab-delimited expression files */

2015-02-27T20:45:01Z

‎Housekeeping Genes Normalizer and tab-delimited expression files

Smith: /* geWorkbench 2.6.0 and prior */

2015-02-27T20:44:23Z

‎geWorkbench 2.6.0 and prior

Smith: /* Cytoscape */

2015-02-11T22:04:07Z

‎Cytoscape

Smith: /* Astex viewer in MarkUs */

2015-02-11T18:28:23Z

‎Astex viewer in MarkUs

Smith: /* PCA and 64-bit Java */

2015-02-11T17:05:19Z

‎PCA and 64-bit Java

Smith: /* PCA */

2015-02-11T16:47:31Z

‎PCA

Smith: /* PCA */

2015-02-11T16:47:09Z

‎PCA

Smith: /* Embedded browser not compatible with 64-bit Java */

2015-02-11T16:45:58Z

‎Embedded browser not compatible with 64-bit Java

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 ====Gatekeeper stops files from running====
-The first time a downloaded file (e.g. a command file) is run, you must tell Gatekeeper to allow it to run.  Please see instructions at [[Download_and_Installation#IMPORTANT_note_for_MacOSX| IMPORTANT note for MacOSX]].
+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 [[Download_and_Installation#IMPORTANT_note_for_MacOSX| IMPORTANT note for MacOSX]].
 ==geWorkbench 2.6.0==

@@ Line 1: / Line 1: @@
 ==Installation - top issues==
 ===Macintosh OSX platform===
 ====Gatekeeper stops files from running====

@@ Line 11: / Line 11: @@
 ==geWorkbench 2.6.0 and prior==
 ===Housekeeping Genes Normalizer and tab-delimited expression files===
-If a gene expression set is loaded 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.
+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===

← Older revision		Revision as of 20:44, 27 February 2015
Line 10:		Line 10:

	==geWorkbench 2.6.0 and prior==		==geWorkbench 2.6.0 and prior==
		+	===Housekeeping Genes Normalizer and tab-delimited expression files===
		+	If a gene expression set is loaded 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===		===MarkUs===

@@ Line 16: / Line 16: @@
 ===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.
 ===Use of incomplete annotation file causes errors in MRA-FET analysis===

@@ Line 39: / Line 39: @@
 ===Astex viewer in MarkUs===
-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 currently 32-bit, so a 32-bit JRE must be installed on the computer to use this applet.  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.
+====Windows====
 ===Cytoscape loading===

@@ Line 21: / Line 21: @@
 ===PCA and 64-bit Java===
-The PCA 3D Viewer does not work with 64-bit Java, which is now the default on all platforms.
+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).
 ===BLAST===

@@ Line 20: / Line 20: @@
 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===
+===PCA and 64-bit Java===
 The PCA 3D Viewer does not work with 64-bit Java, which is now the default on all platforms.

@@ Line 31: / Line 31: @@
 ===Embedded browser not compatible with 64-bit Java===
-Affects: GSEA, MarkUs, Pudge and PCA.
+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).  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.
+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.
-In addition, the MarkUs results display includes the Astex molecular structure viewer Java applet.  For this to run, a JRE must be available which matches that of the browser being used.  For windows, the default versions of Firefox and Chrome are currently (early 2015) 32-bit, so a 32-bit JRE must be installed on the computer to use this applet.  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.
+===Astex viewer in MarkUs===
 ===Cytoscape loading===