-------- Original Message --------
Subject: Re: MorphoJ in Linux
Date: Wed, 28 Sep 2011 14:15:22 -0400
From: Dennis E. Slice <[email protected]>
To: [email protected]
No direct experience with MorphoJ on Ubuntu, but the following might be
relevant and of general value to some:
1) The message suggests you (or the system) are (is) trying to execute
the .jar file. You should be executing java and telling it to use the
.jar file:
java -jar MorphoJ-installer_Unix_Linux.jar
OSX (Mac) appears to automatically recognize the .jar and do the right
thing, though you need to tweak something to provide parameters like
additional virtual-machine memory. In my experience, Windows knows .jar
files, but treats them as archives if downloaded from the internet - my
version of XP, at least. Hence, the two ways to download 3D-ID
(http://www.3d-id.org/downloads). I suppose I should wrap everything in
a .zip file.
Ubuntu should do something reasonable, but you need to check. Does it
have java installed? Can you click or dbl-click on other .jar files?
2) If you did want to run a downloaded file from the internet on
unix/OSX, you need to explicitly set the executable bit (a reasonable
security precaution). E.g., from the command line:
prompt$ ls -l shrink.sh
might show
-rw-r--r--@ 1 dslice staff 1200 Nov 26 2007 shrink.sh
the 'r's mean the user/owner of the file, members of the files "group",
and everyone else ("other") can read the file. The 'w' means the
owner/user can write/change file, but no one else (indicated by dashes).
And, no one, not even the owner can execute the file (this one is a
script/batch file for rescaling a bunch of images). The owner's
permissions are in positions 2-4, the group's 5-7, and everyone else's
in 8-10. To allow, say, yourself (assuming you are the owner) the
ability to execute the script, you would have to change the mode of the
file with "chmod":
prompt$ chmod u+x shrink.sh
prompt$ ls -l shrink.sh
-rwxr--r--@ 1 dslice staff 1200 Nov 26 2007 shrink.sh
Notice the fourth position now has an 'x' meaning the owner, dslice, can
execute the file. It is a bit confusing (to me, at least) that owner
permissions are designated by 'u' for "user", with everyone else's are
indicated by 'o' meaning "other". I inevitably get this wrong when I
haven't done it in a while. Thankfully, 'g' refers to "group"
permissions. The terminal '@' means there are extended attributes not
displayed on this OS and the initial '-' would be the file type -
"regular" in this case, but often 'd' for directory or 'l' for "link" to
another file.
-ds
On 9/28/11 1:41 PM, morphmet wrote:
-------- Original Message --------
Subject: MorphoJ in Linux
Date: Wed, 28 Sep 2011 04:53:30 -0400
From: andrea cardini<[email protected]>
To: [email protected]
Dear morphometricians,
I keep having problems with the installation of MorphoJ in Linux Ubuntu.
This is the latest error message:
The file 'MorphoJ-installer_Unix_Linux.jar' is not marked as executable.
If this was downloaded or copied form an untrusted source, it may be
dangerous to run. For more details, read about the executable bit.
Has anyone else had similar problems? Is there a simple way to get around
this?
Thanks.
Cheers
Andrea
Dr. Andrea Cardini
Researcher in Animal Biology
Dipartimento di Biologia, Universitá di Modena e Reggio Emilia, via Campi
213, 41100, Modena, Italy
tel: 0039 059 2055017 ; fax: 0039 059 2055548
Honorary Fellow
Functional Morphology and Evolution Unit, Hull York Medical School
University of Hull, Cottingham Road, Hull, HU6 7RX, UK
University of York, Heslington, York YO10 5DD, UK
Adjunct Associate Professor
Centre for Forensic Science , The University of Western Australia
35 Stirling Highway, Crawley WA 6009, Australia
E-mail address:[email protected],[email protected],
[email protected]
Webpage:http://sites.google.com/site/hymsfme/drandreacardini
Datasets:
http://ads.ahds.ac.uk/catalogue/archive/cerco_lt_2007/overview.cfm#metadata
--
Dennis E. Slice
Associate Professor
Dept. of Scientific Computing
Florida State University
Dirac Science Library
Tallahassee, FL 32306-4120
-
Guest Professor
Department of Anthropology
University of Vienna
-
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