error message from Structure

[shuang]

I'm trying to install Structure 2.3.3 on a Linux machine. The source code is from the link below.
(http://pritch.bsd.uchicago.edu/struc...structure.html)

After I followed the installation instruction and tried to run ./structure, I received this error message.

-bash: ./structure: No such file or directory

What did I miss?

[gringer]

There are about 15 different file links on that page (including two source packages). Which one(s) did you download specifically?

Can you show the contents of the directory you installed Structure into (e.g. 'ls .')?

[shuang]

I used the file from

Download package with graphical front end:
For UNIX: [Linux],


Here are the content of the directory

drwxr-xr-x 2 502 staff 4096 2010-02-01 15:25 bin
drwxr-xr-x 2 502 staff 4096 2010-02-01 15:47 class
drwxr-xr-x 2 502 staff 4096 2010-02-01 15:28 doc
drwxr-xr-x 2 502 staff 4096 2010-02-01 15:28 images
-rwxr-xr-x 1 502 staff 1912 2010-02-01 15:47 install
drwxr-xr-x 3 502 staff 4096 2010-02-01 15:25 library
-rw-r--r-- 1 502 staff 995 2010-02-01 15:47 readme
drwxr-xr-x 2 502 staff 4096 2010-02-01 15:28 sample
-rwxr-xr-x 1 root root 77 2012-01-08 14:51 structure

[gringer]

Then you downloaded binaries, not source code.

I'm going to assume you've installed this as root using the install link in the extracted files. It has a strange install process, but I guess it'll do. Note that you need to be inside the extracted directory in order to run the program using './structure'.

Could you try the following commands (from the extracted directory), and show the output:

# (from extracted directory, where you extracted the files to)
cat ./structure
ls /usr/local/Structure/
./structure
java -cp class/Structure.jar RunStructure

[shuang]

Below is the output for each command.


cat ./structure

#!/bin/sh
cd /usr/local/Structure/
java -cp class/Structure.jar RunStructure


ls /usr/local/Structure/

bin class doc images library sample


./structure

Exception in thread "main" java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
at sun.awt.HeadlessToolkit.getScreenSize(HeadlessToolkit.java:279)
at Controller.StructureApp.initStructure(Unknown Source)
at RunStructure.main(Unknown Source)


java -cp class/Structure.jar RunStructure


Exception in thread "main" java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
at sun.awt.HeadlessToolkit.getScreenSize(HeadlessToolkit.java:279)
at Controller.StructureApp.initStructure(Unknown Source)
at RunStructure.main(Unknown Source)

[gringer]

This is strange. Your first error message claimed that './structure' didn't exist:

-bash: ./structure: No such file or directory

But this is giving a different message, which indicates that structure has been installed correctly, and it is trying to run:

./structure

Exception in thread "main" java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.

This error message indicates that it's trying to show a graphical display, but you don't have one. Perhaps you're running structure on a ssh connection or something like that.

There is a standalone structure client that works without graphics, but that's not the one you downloaded. If you want to run from the console, then use the 'package without front end' links.

However, if this is your first time running Structure, you'll probably get quite lost without the Java front end. It has a few checks in it to make sure the data files are properly structured, makes it easy to change parameters, provides a workflow that shows multiple projects at one time, and allows you to do some simple graphical summaries of the results.

[shuang]

I re-downloaded a command-line package from

Download package without front end:
For UNIX: [Linux],

cat ./structure
PuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTYPuTTY
(lots of repeats of PuTTY)

Below are the outputs.

ls /usr/bin/aStructure/console/ (where I installed Structure)
extraparams mainparams structure structure_doc.pdf testdata1

./structure
-bash: ./structure: No such file or directory

java -cp class/Structure.jar RunStructure
Exception in thread "main" java.lang.NoClassDefFoundError: RunStructure
Caused by: java.lang.ClassNotFoundException: RunStructure
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
Could not find the main class: RunStructure. Program will exit.

[gringer]

I re-downloaded a command-line package from
Download package without front end:
For UNIX: [Linux]

You really shouldn't be doing that unless you know what you're doing, but anyway...

cat ./structure
PuTTYPuTTYPuTTY

Where are you running this from? The standalone structure binary is not a shell script. It was written in C, and is compiled to a binary for the distributions. If you want to look at the first bit of the file, you need to run something like the following:

grinja@artemis:~/install/structure/console$ hexdump -C ./structure | head -n 2
00000000  7f 45 4c 46 01 01 01 00  00 00 00 00 00 00 00 00  |.ELF............|
00000010  02 00 03 00 01 00 00 00  80 8a 04 08 34 00 00 00  |............4...|

ls /usr/bin/aStructure/console/   (where I installed Structure)
extraparams  mainparams  structure  structure_doc.pdf  testdata1

By convention, non-distribution installed files should be in '/usr/local/bin', but you also shouldn't need to put this anywhere outside your home directory. At least you've mentioned the absolute path.

./structure
-bash: ./structure: No such file or directory

Did you run this from the directory in which you installed Structure? The './' bit tells the shell to completely ignore any path specification and look for something in the current directory. If you want to run structure from somewhere else, you need to run '/usr/bin/aStructure/console/structure', rather than './structure'.

java -cp class/Structure.jar RunStructure
Exception in thread "main" java.lang.NoClassDefFoundError: RunStructure

The standalone binary doesn't use Java. It's a compiled C program, and can be run directly.

The standalone version of Structure is not written for user friendliness. I suggest you try downloading the frontend version of Structure onto the computer you're using (i.e. the one you're sitting in front of -- probably a Windows machine given that you seem to be using PuTTY), and get comfortable with that first. Once you've done that, then you can try playing round with Structure on a remote system.