Seeing: Windows error 2 occured while loading the Java VM

Jalview Discussion
1

I am completely new to JalView.
I am seeing this error whether I run the install with or without Java VM.

I have:

  • Windows 7 64bit [Version 6.1.7601]

  • Java installed Version 8 Update 31 (build 1.8.0_31-b13)

  • VM 4.0.2 build-591240
    (and a number of windows VMs installed mostly so I can run risky looking aps etc in a sandbox like environment)
    but no unix like VM’s.

I suppose the most obvious thing to do is upgrade to whatever version of VMware you are running.
Can it be installed for free and how?

···

Robert Keith Elias, Quebec Qc Canada
--------- I consider ALL arguments in support of my views ---------

2

Hi Keith.

I am completely new to JalView.
I am seeing this error whether I run the install with or without Java VM.

OK. If the windows error 2 is raised when you try and run the installer, then it isn't finding a necessary library in your java installation - which is not good. Presumably java.exe is on your path when you open a command window and type 'java -v' ?

As a work around, you could simply download the 'no vm unix' package and create a .bat file, but it sounds like you might need to fix your install somehow.

I just checked - I have a native windows7 64bit around the same version as yours, and the same java.

The following installer created a functioning Jalview app when run as administrator:
http://www.jalview.org/builds/release/Web_Installers/InstData/Windows_Pure_64_Bit/NoVM/install-jalview.exe

I suppose the most obvious thing to do is upgrade to whatever version of VMware you are running.
Can it be installed for free and how?

I don't think this is a VMWare issue. Correct me if I'm wrong!

Jim.

···

On 26/02/2015 17:06, Keith Elias wrote:

--
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, College of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk
The University of Dundee is registered Scottish charity: No.SC015096

3

Hi Keith.

I am completely new to JalView.
I am seeing this error whether I run the install with or without Java VM.

OK. If the windows error 2 is raised when you try and run the installer,

then it isn't finding a necessary library in your java installation - which
is not good. Presumably java.exe is on your path when you open a command
window and type 'java -v' ?

When I type 'java -v' at the command line I see (via stderr to screen):

Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
Unrecognized option: -v

I tried:

to no effect.

Even tried:
_JAVA_OPTIONS: -Xms1024M
also to no effect.

I also uninstalled and reinstalled java, but note that my configuration
remained the same. I know how to change the configuration in the windows
interface but do not know where the config file(s) is kept.

As a work around, you could simply download the 'no vm unix' package and

create a .bat file, but it sounds like you might need to fix your install
somehow.

I just checked - I have a native windows7 64bit around the same version

as yours, and the same java.

The following installer created a functioning Jalview app when run as

administrator:

http://www.jalview.org/builds/release/Web_Installers/InstData/Windows_Pure_64_Bit/NoVM/install-jalview.exe

I suppose the most obvious thing to do is upgrade to whatever version of

VMware you are running.

Can it be installed for free and how?

.

I don't think this is a VMWare issue. Correct me if I'm wrong!

You are almost certainly correct. I just misunderstood the documentation.

···

On 26 February 2015 at 12:34, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:

On 26/02/2015 17:06, Keith Elias wrote:

--
Robert Keith Elias, Quebec Qc G1P 1G6
--------- I consider ALL arguments in support of my views ---------

4

Hi Keith.

When I type 'java -v' at the command line I see (via stderr to screen):

Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
Unrecognized option: -v

Good enough - at least Java is there. I also presume you can run Jalview from webstart ?

Typing the following should verify that:
javaws http://www.jalview.org/webstart/jalview.jnlp

(you can also launch throug your browser, but if it just downloads the file you need to follow the Open with.. dialog/explorer menu option to open it with the 'javaws' program which lives in the bin directory of your java installation).

You can launch Jalview from the jnlp file without a network connection, so if that works - you are on your way. The only reason you might want to install via installAnywhere is if you are wanting to run Jalview in batch mode from the command line - but there are other ways of doing that, so let me know if you want to take it further.

Hope this helps!
Jim

···

On 26/02/2015 19:14, Keith Elias wrote:

5

Hi Keith.

When I type 'java -v' at the command line I see (via stderr to screen):

Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
Unrecognized option: -v

Good enough - at least Java is there. I also presume you can run Jalview

from webstart ?

Typing the following should verify that:
javaws http://www.jalview.org/webstart/jalview.jnlp

Yes this worked.

(you can also launch throug your browser, but if it just downloads the

file you need to follow the Open with.. dialog/explorer menu option to open
it with the 'javaws' program which lives in the bin directory of your java
installation).

You can launch Jalview from the jnlp file without a network connection,

so if that works - you are on your way. The only reason you might want to
install via installAnywhere is if you are wanting to run Jalview in batch
mode from the command line - but there are other ways of doing that, so let
me know if you want to take it further.

I'd like to get this to work more or less properly, and I need to ask now
(or wait till monday).

I've placed jalview.jnlp as follows:
c:\winbin\jalview\jalview.jnlp
and can get it to run presumably using files from the internet.

I'd like to run from local files.

In my installs deep under c:\users I found 200 plus files like these:

resource\jre\bin\mlib_image.dll"
resource\jre\lib\fonts\LucidaSansRegular.ttf"
resource\jre\bin\msvcr100.dll"
resource\jre\bin\plugin2\msvcr100.dll"
resource\jre\lib\javaws.jar"
resource\jre\bin\dtplugin\deployJava1.dll"
resource\jre\bin\dtplugin\npdeployJava1.dll"
resource\jre\bin\awt.dll"
resource\jre\lib\ext\nashorn.jar"
resource\jre\lib\plugin.jar"
resource\jre\lib\ext\localedata.jar"
resource\jre\lib\charsets.jar"
resource\jre\lib\resources.jar"
resource\jre\lib\ext\cldrdata.jar"
resource\jre\lib\deploy.jar"
resource\jre\bin\server\jvm.dll"
resource\jre\lib\ext\jfxrt.jar"
resource\jre\bin\server\classes.jsa"
resource\jre\bin\jfxwebkit.dll"
resource\jre\lib\rt.jar"

I also downloaded and extracted the contents of:
27,319,038 examples.tar.gz

can either of these resources be copied somewhere relative to
c:\winbin\jalview\jalview.jnlp

to get the program to run locally?

I could also download the contents of http://www.jalview.org/webstart/
(although right this minute I forget how.)

Thanks for your help.

···

On 27 February 2015 at 03:05, Jim Procter <foreveremain@gmail.com> wrote:

On 26/02/2015 19:14, Keith Elias wrote:

Hope this helps!
Jim

--
Friar Broccoli
Robert Keith Elias, Quebec Qc
--------- I consider ALL arguments in support of my views ---------

6

Hi Keith,

If you have run Jalview from webstart once, then you already have everything necessary on your computer to run it again without an internet connection. Just run the .jnlp file and it will do the rest.

Happy Jalviewing.

Geoff.

···

On 27/02/2015 16:46, Keith Elias wrote:

-- 
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology   
College of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
 

The University of Dundee is registered Scottish charity: No.SC015096
7

Hi Keith.

I am completely new to JalView.
I am seeing this error whether I run the install with or without Java VM.

OK. If the windows error 2 is raised when you try and run the installer, then it isn’t finding a necessary library in your java installation - which is not good. Presumably java.exe is on your path when you open a command window and type ‘java -v’ ?

As a work around, you could simply download the ‘no vm unix’ package and create a .bat file, but it sounds like you might need to fix your install somehow.

.

I just checked - I have a native windows7 64bit around the same version as yours, and the same java.

The following installer created a functioning Jalview app when run as administrator:
http://www.jalview.org/builds/release/Web_Installers/InstData/Windows_Pure_64_Bit/NoVM/install-jalview.exe

As already discussed, this didn’t work, but I have succeeded in doing a proper install:

First I needed to uninstall the existing versions of oracle’s Java on my system.

then install your:
http://www.jalview.org/Web_Installers/InstData/Windows_Pure_64_Bit/VM/install-jalview.exe

which I had downloaded

then reinstall oracle’s Java (in my case both 32 and 64 bit versions) which I did from here:
https://java.com/en/download/manual.jsp

Now everything works fine - and indeed some of the problems I was previously having with approvals to run java apps have now magically disappeared.

Hope this feedback proves useful.

···

On 26 February 2015 at 12:34, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:

On 26/02/2015 17:06, Keith Elias wrote:

8

Thanks for persisting here.

I’ve also noticed that the java updates haven’t been taking as they ought to have suggesting a full reinstall may be needed. Looks like you confirmed it !

Keep an eye out for Jalview prerelease announcements. It would be great if you’d consider betatesting the next version’s installer when we have it available !

Jim.

···

Sent from my android device.

-----Original Message-----
From: Keith Elias eliasrk@gmail.com
To: Jim Procter jprocter@compbio.dundee.ac.uk
Cc: jalview-discuss@jalview.org
Sent: Sat, 28 Feb 2015 16:38
Subject: Re: [Jalview-discuss] Seeing: Windows error 2 occured while loading the Java VM

On 26 February 2015 at 12:34, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:

Hi Keith.

On 26/02/2015 17:06, Keith Elias wrote:

I am completely new to JalView.
I am seeing this error whether I run the install with or without Java VM.

OK. If the windows error 2 is raised when you try and run the installer, then it isn’t finding a necessary library in your java installation - which is not good. Presumably java.exe is on your path when you open a command window and type ‘java -v’ ?

As a work around, you could simply download the ‘no vm unix’ package and create a .bat file, but it sounds like you might need to fix your install somehow.

.

I just checked - I have a native windows7 64bit around the same version as yours, and the same java.

The following installer created a functioning Jalview app when run as administrator:
http://www.jalview.org/builds/release/Web_Installers/InstData/Windows_Pure_64_Bit/NoVM/install-jalview.exe

As already discussed, this didn’t work, but I have succeeded in doing a proper install:

First I needed to uninstall the existing versions of oracle’s Java on my system.

then install your:
http://www.jalview.org/Web_Installers/InstData/Windows_Pure_64_Bit/VM/install-jalview.exe

which I had downloaded

then reinstall oracle’s Java (in my case both 32 and 64 bit versions) which I did from here:
https://java.com/en/download/manual.jsp

Now everything works fine - and indeed some of the problems I was previously having with approvals to run java apps have now magically disappeared.

Hope this feedback proves useful.