[ImageJ-bugs] [Bug 985] New: Permissions change and prevent update

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=985

            Bug ID: 985
           Summary: Permissions change and prevent update
           Product: Fiji
           Version: unspecified
          Hardware: Macintosh
                OS: Mac OS
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: glenmac at uw.edu
                CC: glenmac at uw.edu

I'm in the Admin account doing some maintenance and attempted to update Fiji.
Attempted 'Update'
initial error msg tells me that files are read-only, with a list of jar files
from Fiji/jars
Inspected Fiji package contents and find that all but the macros directory have
been set to Read Only for the Admin account. 
Click 'Apply changes" and get error msg "Installer failed:javaio.IOException:
No such file or directory.

I've had this in the past and resorted to reinstall as well as manually
resetting the permissions.

Here is the log file contents:
java.io.IOException: No such file or directory
    at java.io.UnixFileSystem.createFileExclusively(Native Method)
    at java.io.File.createNewFile(File.java:883)
    at net.imagej.updater.FileObject.touch(FileObject.java:872)
    at net.imagej.updater.Installer.start(Installer.java:131)
    at net.imagej.ui.swing.updater.UpdaterFrame.install(UpdaterFrame.java:629)
    at net.imagej.ui.swing.updater.UpdaterFrame$13.run(UpdaterFrame.java:566)

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.5
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-11M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: READ_ONLY

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20141222150235)
Fiji: http://fiji.sc/update/ (last check:20150106031542)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20141216182637)
IMCF Uni Basel: http://sites.imagej.net/UniBas-IMCF/ (last
check:20141116104718)
Morphology: http://sites.imagej.net/Landini/ (last check:20140723075558)

Files not up-to-date:
  9ad834b2 (MODIFIED) 20141219113019 Contents/Info.plist
  b18d577c (LOCAL_ONLY) 20100916121922 macros/Import_Channel_Order3.8a.txt
  f4074bbb (LOCAL_ONLY) 20120702084321 macros/toolsets/BPCounting3g.ijm
  4b3616ac (LOCAL_ONLY) 20150102164711 macros/toolsets/FV_Montage_ACDC2.ijm
  2fe75fec (LOCAL_ONLY) 20131107171559 macros/toolsets/FWHM3.ijm
  83c6c902 (LOCAL_ONLY) 20110928161804 macros/toolsets/Import Channel
Order3.98.ijm
  17d1aba0 (LOCAL_ONLY) 20140404113537 macros/toolsets/Merge HuPro
Quadrants_3b.ijm
  82d9a278 (LOCAL_ONLY) 20131031121151 macros/toolsets/Open and rescale.ijm
  4651471a (LOCAL_ONLY) 20121116153428 macros/toolsets/PIMP_3_Batch.ijm
  0c5c4a4c (LOCAL_ONLY) 20121116153510 macros/toolsets/PIMP_3_Single file.ijm
  c9dd4f5e (LOCAL_ONLY) 20120708135042 macros/toolsets/Placenta%20macro3.ijm
  a4ed32f3 (LOCAL_ONLY) 20130919160119 macros/toolsets/Read tomography log.ijm
  cb9c4438 (LOCAL_ONLY) 20141104113030 macros/toolsets/Stereology_grid2_6.ijm
  269efdaa (LOCAL_ONLY) 20130903082641 macros/toolsets/Time3D.ijm
  3f09c23b (LOCAL_ONLY) 20130814161408 macros/toolsets/Time_rescale.ijm
  d955a886 (LOCAL_ONLY) 20131218150852 macros/toolsets/Utricle_RGB_merge2_1.ijm
  e9126f03 (LOCAL_ONLY) 20120925154335 macros/toolsets/jv.ijm
  20e2cec7 (LOCAL_ONLY) 20140925095705 plugins/Analyze/ICTN_1_6_.jar
  b2afde18 (LOCAL_ONLY) 20140925095734 plugins/Analyze/cell_counter.jar

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