Need to fix Java heap space

to increase available memory in eclipse go to:

Eclipse->Preferences->Java->installed JREs

select the appropiate JRE and select edit.

default VM arguments should be:

-Xms128M -Xmx1024M

Eclipse and Subversion

Eclipse install seemed to go well. Now moving onto subversion- using the directions from the Klein Gould Blog and making notes here.

The new version is called Indigo. Some minor changes. I'll copy, paste and edit the directions here:

Done on my new iMac:

1. Install Eclipse

Installed the new (Indigo) Classic Eclipse 3.7 package from here.
The new beta version of Eclipse is Ganymede: http://www.eclipse.org/epp/ganymede.php

(I don't think I installed the IDE version: Eclipse IDE for Java Developers.)

Eclipse opens properly from quicksilver.

I have Java 1.6 preinstalled and I'm hoping that will work.

2. Install Subversive plugin

The relevant links are on this site:

http://www.eclipse.org/subversive/downloads.php

Here is some helpful info from that site:

"Subversive distribution consists of two parts - Subversive plug-in and Subversive SVN Connectors. Both parts are required in order to work with Subversive. Subversive plug-in is provided under the terms and conditions of the Eclipse Public License Version 1.0 ("EPL"). A copy of the EPL is available at http://www.eclipse.org/legal/epl-v10.html. Subversive SVN Connectors are external libraries with their own licenses, which are distributed from an external location at www.polarion.com. "

So Eclipse already knows about the Plug In update site and you just need to find and install it:

Go to eclipse.

Go to Help ->Install New Software

Click on the blue "Available Software Sites" Link and find the Subversive update site which should be this:

http://download.eclipse.org/technology/subversive/0.7/update-site/

Edit this to name it something like "Subversive" and click OK. Then make sure that it is checked on the list.

(Don't know if this is necessary, but I highlighted it and clicked "Reload.")

Now click OK to go back to the install dialogue. Select the Subversive link on the drop down box labeled "Work With."

Three choices should pop up. I'm installing all three, though I think the most important (maybe the only important) choice is the "Subversive SVN Team Provider Plugin." Click at least this option and click Next, Next, Accept Terms, then Finish.

Takes a few minutes to install. Requires restart. Upon restart, an SVN connections installation dialogue will pop up.

3. Install Subversion Connectors

More info from above site:

"In order to install Subversive you should install Subversive plug-in and at least one Subversive SVN connector, such as native (win32 only) JavaHL connector or pure Java SVNKit connector. Subversive plug-in and Subversive SVN Connectors are distributed from different update sites on different locations, so you should point two update sites in Eclipse update manager. "

Not sure which connector to install (though you definitely need the Connectors and a KIT), so I installed them all directly from the pop-up box. (Click next, next, agree, next or finish.) Agree to the security check.

Requires restart.

Could also paste a new link under the Help-> Install New Software box. The update site is

http://community.polarion.com/projects/subversive/download/eclipse/2.0/update-site/

which is located on the polarion site:

http://www.polarion.com/products/svn/subversive/download.php?utm_source=eclipse.org&utm_medium=link&utm_campaign=subversive

(This step should probably be done (or checked) anyways so that Eclipse knows where the website is to look for updates.)

4. Import SciKit from the repositories

In Eclipse, go to File -> Import.

Expand SVN and select "Projects from SVN"

Enter the URL for SciKit which is this:

http://scikit.googlecode.com/svn/


(The project homepage for SciKit is here: http://code.google.com/p/scikit/

You can go there and click on Source to find the URL. This is a public project, so you shouldn't need a password.)

Click on browse.

Highlight "trunk" and click finish.

Click Next and Finish until finished.

Some kind of message that a new master password was created. Created new questions and answers. Not sure what that was about?

5. Import Klein-Gould code from the repositories.

Pretty much the same thing:

Go to File -> Import.

Expand SVN and select "Projects from SVN"

Click on "Create a new repositiory location".

Enter the URL for the Klein Gould code which is this:

https://klein-gould.googlecode.com/svn

(The project homepage for SciKit is here: http://code.google.com/p/klein-gould/
You can go there and click on Source to find the URL. This is a NOT a public project, so you do need a password which you can get from this site under source and regenrate it if needed. You must be a member to access this.)

Expand "trunk" and only highlight "JavaSims" (not Kip's code.)

Click Next and Finish until finished.

You might want to fix things up a bit by clicking on Package Explorer Menu (the little white down arrow in the upper right corner of the Package Explorer) and clicking Package Presentation -> Heirerchical.

You can also change the keyboard bindings by clicking Eclipse -> Preferences -> General -> Keys and then changing Scheme to Emacs.

Now, everything should be perfect!

Aquaterm

Aquaterm install says successful

Eclipse Install

Eclipse install seems fine. Put in my local applications directory. But Java on iMac is version 1.6.0 JRE and I would like to have JDK, but I can't find downloads on the usual oracle website:

http://www.oracle.com/technetwork/java/javase/system-configurations-135212.html

So I'm leaving this as is for now. Not updating my code yet because I think I haven't updated on my laptop in a while.

macports installs fail

I get a similar error when trying to install gnuplot using MacPorts:

Error: Target org.macports.activate returned: could not read "/tmp/mpextractcQi0GNq7/opt/local/share/man/man3/bn_print.3ssl.gz": no such file or directory
Error: Failed to install openssl
Log for openssl is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_devel_openssl/openssl/main.log
Error: The following dependencies were not installed: gd2 xpm xorg-libXext xorg-libX11 xorg-libxcb python27 openssl python_select readline sqlite3 python27 xorg-libpthread-stubs xorg-xcb-proto libxml2 xorg-util-macros xorg-xcmiscproto xorg-xextproto xorg-xf86bigfontproto xorg-xtrans xorg-libXt xorg-libsm xorg-libice pdflib
Error: Status 1 encountered during processing.


May try homebrew and see how that works.

Installing mactex and diversions

Readme for mactex install includes:

A custom install option is provided for users who want only part of the package. In particular, the package contains Ghostscript and the "convert" utility from Image Magick; users who already have Ghostscript and the full Image Magick may want to use custom install to avoid the versions provided here. The Latin Modern and TeX Gyre fonts are part of TeX Live and automatically available in TeX; by using custom install you can also install them in the system font folder and make them available to all Macintosh applications.

So I think I may try to install ghostscript and imagemagic separately. I want to try to put everything in the right places from the beginning so I don't have too much clutter.

Here's an article on why you should install into usr/local instead of usr/bin.

http://hivelogic.com/articles/using_usr_local/

I'm going to go ahead and choose MacPorts over Fink, based on the impression that I get from the blogs that it is more up to date. Looks like Homebrew is a good option too. We'll see...

Using this site.

Had to register as a mac developer to get access to Xcode which is needed for MacPorts. Don't remember having to do this for Fink. But it looks like homebrew requires this too.

Install successful (not tested)

Macports install successful (not tested)

Used MacPorts to install ImageMagick and got the following errors:

Error: Target org.macports.activate returned: could not read "/tmp/mpextractZQRpVIRz/opt/local/share/man/man3/bn_print.3ssl.gz": no such file or directory
Error: Failed to install openssl
Log for openssl is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_devel_openssl/openssl/main.log
Error: The following dependencies were not installed: ghostscript xorg-libXext xorg-libX11 xorg-libxcb python27 openssl python_select readline sqlite3 python27 xorg-libpthread-stubs xorg-xcb-proto libxml2 libxml2 xorg-util-macros xorg-xcmiscproto xorg-xextproto xorg-xf86bigfontproto xorg-xtrans xorg-libXt xorg-libsm xorg-libice lcms liblzma p7zip urw-fonts
Error: Status 1 encountered during processing.

-convert command not found in bash.... will look into this later.

Installing MacTex (small convert package, I think). Successful install it seems.

Zotero

Added zotero add on to firefox. Will still use zotero for now, though I'm going to check out the new projects eventually.

Starting with latex

Installing texshop- should be a complete tex install from here:
http://pages.uoregon.edu/koch/texshop/obtaining.html

Also,
Here's a nice online tool that makes images from latex:
http://maru.bonyari.jp/texclip/texclip.php

Rachele loves her new iMac

New positive attitude this time. Brand new iMac for my brand new job with a 3.4 GHz Intel Core i7 processor and giant 27 inch screen. OS X 10.6.8.

So far, I've got standard Mac software (including the iWork programs) and the word package that I need for teaching. Here's what I need to add:

Programing:

compilers (esp fortran)
Newest version of eclipse
Gimp
Mathematica or Maple- whatever they have
Terminal (?)
Aquamacs(?)
Texmacs
Latexit

I want to set up everything that I can that has a direct mac install before I try working on Fink or equivalent. Will post updates on how everything goes.

Time Machine Dead Again

Don't know how long it's been since I've backed up. Whenever TM tries to back up, I get the error

"Time Machine Error
The backup disk image could not be mounted."

I have had this problem before, and I think I may have totally started over (built a new sparse bundle) which I don't want to have to keep doing. LAME.