Sceeter bites

Mama:  Why do you have so many mosquito bites, baby?  Is it because you're so sweet?
Mila:  No, it's because a bug bit me.

New MacBook Pro

Initiating New MacBook Pro

System Preferences:
Changed trackpad gestures and keyboard shortcuts
VPN from BU (link with directions on previous post)
Show all files in finder:  http://www.macworld.com/article/1051830/showallfinder.html

Installed software:
TexShop
Skype
Quicksilver
Picassa
Dropbox

Programming:
XCode?
Gnuplot?
Eclipse (Classic Eclipse 4.2)
Subversion

Eclipse and Subversion

I'm copying and pasting and then editing installation of eclipse and subversion for the setup on the right computer in lab.

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 3.7.2 package from here.

I downloaded classic, not the developers version.

Paste the whole folder in Applications.  

Eclipse opens properly from quicksilver.

I have Java 1.6.0_31 preinstalled.

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.   "

Go to eclipse.

Go to Help ->Install New Software

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

---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.

UPDATE:  This link is NOT THERE, so I'm adding it and calling it "Subversive Update Site"

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 (4) 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.)

UPDATE:  This is site is already installed.

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.

(Some warning about normalizing stuff.  Ignored.)

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!

Trying to get Pyxplot

Reacquainting myself with homebrew:

https://github.com/mxcl/homebrew/wiki/FAQ

Ran "brew update" and "brew upgrade."

Having problems with "brew doctor".  Finally fixed the brew doctor error by doing a git clean -- using this post:

https://github.com/mxcl/homebrew/issues/11761

Now it says my system is raring to brew, but it still won't install latex2html.  Not even sure this is what I need, but it says that latex2rtf is already installed and latex2html is the only other package listed under "brew search latex."

I'm downloading MacTeX to see if that helps.  I DO already use TexShop just fine, so I know I have latex somewhere.

rdominguez5359:pyxplot-0.8.4 racheledominguez$ ./configure
Checking for latex             ............. NO
ERROR: Required program latex could not be found.
rdominguez5359:pyxplot-0.8.4 racheledominguez$ 

Fixed this by moving the folder into /usr.

Now I get:

Last login: Fri May 25 12:23:45 on ttys005
rdominguez5359:pyxplot-0.8.4 racheledominguez$ ./configure
Checking for latex             ............. YES
Checking for ImageMagick convert............ YES
Checking for sed               ............. YES
Checking for gunzip            ............. YES
Checking for wget              ............. NO
WARNING: wget could not be found. Installation will proceed, but PyXPlot will not be able to plot files directly from URLs.
Checking for ghostscript       ............. YES
Checking for ghostview         ............. NO
Checking for ggv               ............. NO
Checking for GNU make          ............. YES (make)
Checking for gcc               ............. YES
Checking for libreadline-dev   ............. YES
Checking for libcfitsio-dev    ............. NO
Checking for libgsl0-dev       ............. ./configure: line 227: gsl-config: command not found
NO
ERROR: Header files for required library 'libgsl' could not be found.
rdominguez5359:pyxplot-0.8.4 racheledominguez$

Homebrew has wget, but none of the others, so I am going back to MacPorts.

Have to install the new version for Lion.

Ran selfupdate.

Able to get most of what I needed:

rdominguez5359:pyxplot-0.8.4 racheledominguez$ ./configure
Checking for latex             ............. YES
Checking for ImageMagick convert............ YES
Checking for sed               ............. YES
Checking for gunzip            ............. YES
Checking for wget              ............. YES
Checking for ghostscript       ............. YES
Checking for ghostview         ............. NO
Checking for ggv               ............. YES (ggv, don't forget to set "watch file" in the viewer preferences!)
Checking for GNU make          ............. YES (make)
Checking for gcc               ............. YES
Checking for libreadline-dev   ............. YES
Checking for libcfitsio-dev    ............. YES
Checking for libgsl0-dev       ............. YES
Checking version of libgsl0-dev ............ YES
Checking for libfftw3-dev      ............. YES
Checking for gunzip            ............. YES
Checking for libxml2-dev       ............. YES
Checking for libpng-dev        ............. YES
Checking for libkpathsea-dev   ............. NO
Checking for kpsewhich         ............. YES
Configuration successful.
To continue installation, type 'make'.


But I still don't know how to get the final two dependencies.

Installed all of these packages from Macports:

cfitsio, fftw-3, ghostscript, gsl-devel, gv, ImageMagick, libpng,
libxml2, readline-5, texlive, wget, zlib.

and I'm still missing libkpathsea-dev.

OK-weird.  Now my config file gives:

rdominguez5359:pyxplot-0.8.4 racheledominguez$ ./configure
Checking for latex             ............. YES
Checking for ImageMagick convert............ YES
Checking for sed               ............. YES
Checking for gunzip            ............. YES
Checking for wget              ............. YES
Checking for ghostscript       ............. YES
Checking for ghostview         ............. YES (gv, double hyphen options)
Checking for ggv               ............. YES (ggv, don't forget to set "watch file" in the viewer preferences!)
Checking for GNU make          ............. YES (make)
Checking for gcc               ............. YES
Checking for libreadline-dev   ............. YES
Checking for libcfitsio-dev    ............. NO
Checking for libgsl0-dev       ............. YES
Checking version of libgsl0-dev ............ YES
Checking for libfftw3-dev      ............. NO
Checking for libfftw2-dev      ............. NO
ERROR: Header files for required library 'libfftw' could not be found.

I don't know why this is different from before.

Upgrade to Lion

My IT guy did this for me, so everything seems to be running smoothly so far. Here are a few notes of a few extra things I needed to do.

Terminal here:

Found this:

As of Mac OS X Lion 10.7, Terminal includes exactly this functionality as a Service. As with most Services, these are disabled by default, so you'll need to enable this to make it appear in the Services menu. System Preferences > Keyboard > Keyboard Shortcuts > Services Enable New Terminal at Folder. There's also New Terminal Tab at Folder, which will create a tab in the frontmost Terminal window (if any, else it will create a new window). These Services work in all applications, not just Finder, and they operate on folders as well as absolute pathnames selected in text. Keyboard shortcut not working Tried installing the new version of XCode, but then uninstalled and just installed the command line tools from here: https://developer.apple.com/downloads/index.action# Finally got homebrew installed, but still have warnings: rdominguez5359:local racheledominguez$ brew doctor Warning: /usr/local/include isn't writable. This can happen if you "sudo make install" software that isn't managed by Homebrew. If a brew tries to write a header file to this directory, the install will fail during the link step. You should probably `chown` /usr/local/include Warning: /usr/local/share isn't writable. This can happen if you "sudo make install" software that isn't managed by Homebrew. If a brew tries to write a file to this directory, the install will fail during the link step. You should probably `chown` /usr/local/share Warning: Some directories in /usr/local/share/man aren't writable. This can happen if you "sudo make install" software that isn't managed by Homebrew. If a brew tries to add locale information to one of these directories, then the install will fail during the link step. You should probably `chown` them: /usr/local/share/man /usr/local/share/man/de /usr/local/share/man/de/man1 /usr/local/share/man/man1 Finally installed gnuplot with brew install gnuplot. Gnuplot success!

VPN connection on Office iMac

http://www.bu.edu/tech/accounts/remote/vpn/use/mac/

So easy!