Category Archives: OSX

MarkDown QuickLook MacOS

Donald G. McGahan
September 14, 2017

This post is about getting MacOS to preview my markdown file when I have the file highlighted in the finder and hit the spacebar. This is called quicklook in MacOS terminology. I need to apply this over several machines so here is why and what I’ve done.

My filesystem is starting to become quite populated with plane text files where I use a flavor of  John Gruber’s MarkDown to enhance the utility of what final display format I intend for the content to be delivered in.

I have more than one MacOS application that I have been using as crutches when creating or modifying these text files with MarkDown. One is Byword and the other is Fletcher Penney’s  MultiMarkDown Composer.

These files are truly plane text and the file extension might just be “.txt” and indeed this works just fine. However, if given a unique extension the OS can be instructed to view and open the text files that I have sprinkled with markdown in one of my helper applications.

The frustration I was having is that I had files with extensions including  md, mmd, and markdown. John Gruber and Fletcher Penney favor markdown. I see the advantages of using markdown as the extension and will likely adopt that moving forward.

The issue with quicklook not rendering a, quicklook, for the different markdown extensions I am using. While there may be a more elegant way to address this what I found is a GitHub repository by Phil Toland for QLMarkdown which I applied using homebrew at the MacOS Terminal app.

$ brew cask install qlmarkdown

Audio file from text with OSX say

A say example:

Using terminal navigate to the directory where the source file is at.

say -v Ava -o "audio_file_created.aiff" -f "file_to_read.txt"

-f tells the program to read the file following in parenthesis
-o tells the program the output file to record to.
-v is the voice to use

Personally I use another app to convert to mp3 since that is small and fairly ubiquitous.

To use wave as the output (-o) navigate to the source directory. Then add –data-format=LEF32@8000 after the output file.

 say -v Ava -f "Findings_about_Research-R2_JGnKS.txt" -o Findings_about_Research-R2_JGnKS.wav --data-format=LEF32@8000

This sounds lousy though. I prefer to use Quicktime 7 and convert.

More can be learned from a web search, but this is a note to self.

Terminal Utilities

The terminal is a kinda scary place for many a Apple MacIntosh user. It does not have to be. Sometimes searching the web to find a nice presentation that I have seen previously is tedious. Consider the list below as a ‘note to self’ kind of repository.

Mitchinme has a list of eight terminal (command line) utilities at [ Last Accessed July 29, 2016 ]

Arthur Gareginyan at has an explanation of how to use the ‘find’ with terminal to identify zero sized (empty) files and folders. [ Last Accessed July 29, 2016 ]

Mike Rubel has an article at [ Last Accessed July 29, 2016 ] that is specific to ‘rsync’ that does not presume that the reader is an expert but does that the reader has familiarity with the terminal (command line). has a commendable repository [Last accessed August 2, 2016 ] and some we find necessary, but sometimes esoteric, are listed below:

  • Find Duplicate Files (based on MD5 hash) — For Mac OS X HERE

More to come.

Installing R in OS X with Homebrew and Cask

Installing R in OS X with Homebrew and Cask

I can install the R language for statistics and environment for statistical computing and graphics from the CRAN site and it is a simple install from the CRAN site and probably recommended for most folks.

I wanted to build it from source, but doing so without a safety net  was beyond the investment, in time to refresh my build from source skills, that I was willing to make. With Homebrew and the Homebrew Cask add-on it is definitely approachable. It still takes more time that the CRAN install, but less technical input and the time investment is copy and pasting the commands into the terminal and waiting, considerable waiting, for each program to be compiled.

The compiling time for me was on my MacAir with i7 and it did warm up and employ the fan. I followed the fine outline provided by Bob Rudis aka “hrbrmstr” with a Twitter handle by the same. I ran across his blog-post on R-bloggers titled Installing R on OS X – “100% Homebrew Edition” of date October 22, 2015, and is actually a duplicate from with the same title.

The following is lifted directly from Bob Rudis’s posts. Tip of the hat to ya’ Bob. I have placed it here so that I have easy access. Please go to his posts to get his excellent notes.

brew tap caskroom/cask
brew install brew-cask
brew install Caskroom/cask/xquartz
brew cask install java
brew tap homebrew/science
brew install R
brew install Caskroom/cask/rstudio
# For latex:
brew cask install mactex
brew cask install basictex # suggested by @noamross
brew install libsvg curl libxml2 gdal geos boost
R CMD javareconf JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers
brew tap caskroom/fonts
brew cask install font-fira-code
brew cask install iterm2


when running brew update sometimes it reports that /usr/local is not writable. Then run

sudo chown -R $(whoami) /usr/local

That’s it.

Talk Back prose or prose poetry

Talk Back prose or prose poetry

SpeechnDictationIconWant to have a second read of something you have written?
Kind of a dispassionate editor type of read?
Here is a way to make your writing read more polished.

When I write, I have an inner dialog which I put to words on paper, well not so much paper as into a text editor or word processor nowadays. I notice that when someone else would read it out-loud it frequently does not carry the same cadence and emphasis that it did in my inner dialog.

I have noted these discontinuities and questionable meanings with others writings also. These are readily identified in others writing wether I read there work out-loud or silently. I often think, “What are they trying to say?” when reading new scientists writings, and especially with students submissions.

With student mentees drafts, I would expect some rough spots like these, but they happen overly often, and go unidentified by the author, lingering over many drafts (that is when I can get them to submit more than one draft :-). So, I recognize that it is hard to track down discontinuities and questionable meanings and fix them: especially with the very compressed turnaround time we work with for todays communications.

I have found that if I use a text to speech feature on my Apple OSX computer I can fix many of these in my own writing. I have long been using text to speech as a tool with face to face editing sessions with student mentees and they have very positive responses.

How to enable text to speech.

OSX computer — interpret OSX to mean a Mac

With an OSX computer it is easy to have the computer speak selected text. Just go to “System Preferences” and choose the “Dictation and Speech” icon, choose the “Text to Speech” button and check the “Speak selected text when the key is pressed box.” The default is Option+Esc key combination and that has worked fine for me — your mileage may vary — but you may choose another key combination. Just select some text, and Option+Esc key combination.


On the iPad it is only slightly more work to turn on this great feature.

Launch “Settings” (the icon of a gear) and choose “General” then choose “Accessibility” and toggle “Speak Selection” to on. I the “Speak Selection” dialog window the voice used and the “SPEAKING RATE” can be adjusted. I like the “Highlight Words” being set to on but you can turn it off. With “Speak Selection” set to on, when text is highlighted “Speak” is an option on the popup dialog. Happy Days. (This works for the iPhone as well.)

Windows 7

Open the “Ease of Access Center” window by pressing the Windows key + U, or by clicking the “Start” button, choose “Control Panel,” then choose “Ease of Access,” then choose “Ease of Access Center.” Under the “Quick access to common tools” header click ‘Start Narrator‘, or press Alt + N. (This will start Narrator for current use and to make Narrator start automatically when you log in, with the “Ease of Access Center” window open. Under the “Explore all settings” header, click on “Use the computer without a display,” or press Tab until it is highlighted and then press Enter.

Keyboard shortcuts in Windows 7 Narrator

To read text from a screen, use the following shortcuts when Narrator is running.

    • Insert + F3 – Read the current character.
    • Insert + F4 – Read the current word.
    • Insert + F5 – Read the current line.
    • Insert + F6 – Read the current paragraph.
    • Insert + F7 – Read the current page.
    • Insert + F8 – Read the current document.

There you go. Clear as mud. Lots of key combinations to remember.

Windows 8

In Windows 8 Microsoft has moved in the direction of complexity as there are different ways to get Narrator turned on depending upon the device.

  • On the sign-in screen, press the “Windows logo key+U” or click the “Ease of access” button in the lower-left corner, and then choose “Narrator.”
  • On a keyboard, press the “Windows logo key+Enter.”
  • On a touch-only device, hold down the “Windows logo button and press the “Volume Up” button.

I like this description the best (probably because I have used Windows since before there was Windows 🙂

Settings > Control Panel > Ease of Access > Speech Recognition


Most modern devices have text to speech capabilities so the device is not the issue. The iPad is best at being used to consume and digest information, with only modest “creating and authorship” capabilities. This lends it well suited to using it as a tool to assess the readability of ones one work.

Add a little color to Macs Terminal

I added a little color to Mac Terminal.

Here is how.

To edit the file(s) use:

nano ~/.bash_profile
nano ~/.bashrc

If no .bash_profile and .bashrc the do the following to create them.

In the Terminal enter:

touch ~/.bash_profile
touch ~/.bashrc

Then you can use nano to edit the files.

Add the following to the .bash_profile

export PS1="\[\033[36m\]\u\[\033[m\]@\[\033[32m\]\h:\[\033[33;1m\]\w\[\033[m\]\$ "
export CLICOLOR=1
export LSCOLORS=ExFxBxDxCxegedabagacad

To immediately enable any changes in the file .bash_profile use source:

source ~/.bash_profile

This will assign a new set of colors to the terminal text.

Screen Captures using a Mac

OSX Preview and Grab application icon images
OSX Preview and Grab application icon images

Screen Captures using a Mac

Windows users often tell me about the Sangit application available from TechSmith. This program is available for OSX also, but is an extra expense.

The synopses is that an application/program to capture screenshots is built into the OSX operating system. Using Sangit does not preclude using Grab, and visa versa.

Currently I am using the Mavericks OS (10.9) but much of this works in previous versions of OSX.

If your the non-technical type, jump to the “Creating a Screen Capture image from within Preview” section below.

Grab the app

I have been using the great application “Grab” for quite some time. Grab is found using the Finder in Applications –> Utilities and when using the Launchpad in/on the Dock in Other. The icon is a pair of scissors overlaying a square depiction of a screen.

Four options to capture screen content exist once the Grab application is started: SelectionWindowScreen, and Timed Screen. And you choose between these from the Capture pulldown menu.

Key Combinations to “Grab” Screen Captures

You can place the Grab icon in the Dock if easy access, but invoking the program from the icon (via the graphical user interface [GUI]) is not the only way to use this handy app. You can also use key combinations.

Several options for screen capture are possible. One thing the new user of this app should probably be aware of is that images captured using the keyboard shortcuts are stored on the desktop by default. This can be changed, and the “how-to” is below. First, however, how to use those keystroke keyboard shortcuts! Here they are:
  • CMD+Shift+3 will capture the entire screen and save it as a file.
  • CMD+CTRL+Shift+3 will capture the entire screen and copy to the clipboard.
  • CMD+Shift+4 will capture an area that you select and save it as a file.
  • CMD+CTRL+Shift+4 will capture an area that you select and copy it to the clipboard.
  • CMD+Shift+4 then space will capture a full window, menu, desktop icon or the menu bar with drop shadows and save as a file.
  • CMD+CTRL+Shift+4 then space will capture a full window, menu, desktop icon, or the menu bar with drop shadows and copy to the clipboard.
  • Holding down the SPACE key after you start drawing an area will allow you to reposition it.
  • Holding down OPTION right after you start drawing an area will allow you to adjust the width and height of the selected area.
  • Hit ESC while capturing an area or window to exit the capture mode.
Todays average personal computer user is so pampered and unsophisticated (yes that sounds harsh, but it is the truth) that they don’t realize that most apps and programs have some very powerful and handy keyboard shortcuts. These save tons of time in the long run with an investment of a little memorization of the keyboard shortcuts.

Change “save to” locations of Grab key combinations

Alright, back to the issue of the keyboard shortcut invoking of the app’s saving to the desktop. I like to keep my desktop as uncluttered as possible. It is hard to do, but one can always try :-). You can easily change the location using the following terminal commands.
defaults write location ~/Downloads

Then again in the terminal

killall SystemUIServer

This will change the default location to the Downloads folder. Another location can be chosen if desired.

The pictures are saved as tiff format. Use Preview to open and then save them in an alternative format if desired.

 Creating a Screen Capture image from within Preview

You can easily just do this all from within Preview.

  • Start Preview using one of the methods below
    • Finder>Applications>Preview
    • Click the Preview Icon in your Dock
    • Search Preview in Spotlight
  • At the top of your screen, click on File in the drop down menu.
  • At the bottom of the drop down menu, hover your mouse over the text ‘Take Screen Shot”
  • You will see a choice of:
  • From selection
  • From window
  • From entire screen

Preview has tools to annotate the screen capture picture.

Converting text formats with OS X terminal

It is handy to be able to convert from one text format to another.

It is probably very common that the ‘right tool for the job’ is not often applied with it comes to digital files. This is likely because of impatience and being unfamiliar with the proper tool.

I have seen several instances where someone will load up a word processor, waiting several seconds for it to get to a ready state, and then fuss with opening menu after menu to try and accomplish converting the file.

This seems inefficient and cumbersome.

With the OS X operating system it is a snap to accomplish this type of task using a command line tool called ‘textutil’.

This ‘textutil’ can write out as txt, html, rtf, rtfd, doc, docx, wordml, odt, or webarchive.

Personally I have many times written a web page html and want to make a rtf document.

Open the Terminal (an easy way is to begin to type terminal in Spotlight) and enter:

textutil -convert FORMAT path-to-the-original-document

Replace FORMAT with txt, html, rtf, rtfd, doc, docx, wordml, odt, or webarchive.

This will place the converted file in the same directory as the original  file.

Installing Homebrew

I chose to install Homebrew and let it due the heavy lifting for adding packages.

First Xcode needed to be installed from the Apple Applications Menu.
Then start Xcode and accept the agreement or Homebrew will moan.
I installed Homebrew using the terminal command at their site.

Following the Homebrew installation run:

brew update

brew doctor

And possibly fix the items mentioned in brew doctor. Some do not need fixing and are only warnings.

After that simply run:

brew update && brew upgrade

But see the add-on below.

The next suggested addition is Cask. Cask extends Homebrew to allow managing the installation of graphical applications using the command line.

To get the add-on Cask run:

brew tap caskroom/cask

Then the way to update is to simply run:

brew update; brew cleanup; brew cask cleanup

Installing GNU Emacs

I choose to install GNU Emacs using Homebrew.

The El Capitan (10.11.2) OS X version has Emacs 22 builtin but I wanted some GUI integration.

At the command line I ran this command:

brew install emacs --HEAD --use-git-head --cocoa --srgb

I let if finish and then to integrate a nice icon to start Emacs from the applications menu I ran this command:

brew linkapps

I wanted to be able to easily run both Emacs 22 and Emacs 25 from the command line in addition to the GUI GNU Emacs 25.

Check if their is a .bash profile.

In the Terminal enter:

ls -al ~

If no .bash_profile and .bashrc the do the following to create them.

In the Terminal and enter:

touch ~/.bash_profile
touch ~/.bashrc

To edit the file(s) use:

nano ~/.bash_profile
nano ~/.bashrc

To the .bashrc add:  [ -r ~/.bash_profile ] && source ~/.bash_profile

To the  .bash_profile add:

alias emacs25="/Applications/ -nw"
alias emacs22="/usr/bin/emacs"

These alias allow me to run emacs in the terminal for either version. in the terminal by adding the version number to the end of emacs (’emacs22′ or ’emacs25′). To get the GUI version don’t add the version number ’emacs’.

To immediately enable any changes in the file .bash_profile use source:

source ~/.bash_profile

Freshen up rsync

I wrote about rsync in 2009 in a previous post when the OS X was Leopard (10.5).

Generally, I have been pleased with the performance of the version that ships with each successive OS X version. As of the writing of this post I am using El Capitan (OS 10.11.1) on my Mac Air 11″ and as usual the version of rsync works. Now I want to use the latest version to take advantage of better memory management and faster performance.

I want to leave the rsync (version 2.6.9) that ships with the OS in place so that if anything is dependent upon it things won’t break. I simply want to add the new version.

If the package manager Homebrew is installed it is easy to add the newer rsync (3.1.1 in this case). If Homebrew is not installed then install it. Simply paste the following into the terminal prompt.

brew tap homebrew/dupes

brew install rsync

Then edit /private/etc/paths to put /usr/local/bin before /usr/bin

nano /private/etc/paths

That is it. To run the older version of rsync the entire path must be explicitly stated.



Installing MacQIIME

Generally, the MacQIIME page by Jeff Werner seems like a reasonable start. The installation instructions are reasonably clear, but these directions are not for an absolute beginner using a Mac. Particularly it is probably best if the user has some knowledge of *NIX flavor operating systems.

My journey started by following Jeff Werner’s instructions, but I deviated.

I had a problem with the installation because the script wants to place the macqiime file in /usr/bin. This folder is restricted in this OS X El Capitan (10.11.1) version. Therefore, I modified the install.s file to put macqiime in /usr/local/bin:

cd [PATH to]/MacQIIME_1.9.1-20150604_OS10.7

nano install.s

Change all instances of /usr/bin to /usr/local/bin and save (write out) and exit.

I had already added /usr/local/bin to my PATH

To check the PATH

echo $PATH

If it is not in the path add to path with

export PATH=”/usr/local/bin:$PATH”


An important part is probably at the bottom of his MacQIIME page:

Not included, but may be needed: You’ll probably have to install or update XQuartz; Legacy NCBI blast is not installed (assuming many people have their own install of this); AmpliconNoise is not installed (it requires custom compilation, dependent on MPI, specific to your system); USEARCH is not installed, due to licensing; R and associated functions are not installed.

I walked through the addons. XQuartz had a dmg. Java installation was pretty straight forward. I had an install of R and adding packages was no trouble at all. But some addons require some work in the terminal.

I choose NCBI blast-2.2.25-universal-macosx.tar.gz and used option 2 and put it in my machines opt folder instead of my document folder. These instructions were fairly clean.

USEARCH installation instructions rely on those of the USEARCH site and are not as clean.  Keeping a window or tab open to the blast install instructions from Jeff Werner’s site helped with the terminal commands necessary to accomplish moving the files and renaming them at the same time. Because I chose to place them in opt I had to preface the copy (cp) command  and the change permission command (chmod) with sudo and run it as administrator:

sudo cp Download/usearch5.2.236_i86osx32 /opt/usearch

sudo cp Download/usearch6.1.544_i86osx32 /opt/usearch61

sudo chmod +x /opt/usearch

sudo chmod +x /opt/usearch61

Adding these locations to the path:

export PATH=$PATH:~/opt/usearch

export PATH=$PATH:~/opt/usearch61

Check that the PATH has these added

echo $PATH

The AmpliconNoise installation in Jeff Werner’s instructions are non-existent.

I chose to install Homebrew and let it due the heavy lifting.

First Xcode needed to be installed from the Apple Applications Menu.
Then start Xcode and accept the agreement or Homebrew will moan.
I installed Homebrew using the terminal command at their site.

Following the Homebrew installation run:

brew update

brew doctor

Fix the items mentioned in brew doctor. For this installation:

sudo chown -R $(whoami) /usr/local/share/man/mann

Install GNU Science Library with Homebrew

brew install gsl

The next addon is AmpleconNoise. When downloaded and unpackaged it contained a Doc.pdf that stated it had dependencies.

It needs open-mpi and that is available from Homebrew:

brew install open-msi

It needs GNU Science Library and that is already installed. But it also requires mafft. This formula was found in a tap. To install it, run:

brew install homebrew/science/mafft

AmpliconNoise make fails with

FCluster.c:675:3: error: non-void function ‘outputCluster’ should return a value [-Wreturn-type]

A report of this is was at

This may be related to Xcode so I went to and downloaded the Command Line Tools (OS X 10.11) for Xcode 7.2 beta and installed Command_Line_Tools_OS_X_10.11_for_Xcode_7.2_beta_2.dmg manually. However, running ‘make’ on the ApliconNoise folder still returns this error.

With some help from Yoshiki Vázquez Baeza at the QIIME help group with a solution.

Can you try going to the FCluster folder and opening the file named makefile to change the second line to look like this:

CFLAGS = -O3 -Wno-error=return-type

This should show you a warning instead of the error you are seeing. Try re-running the make command again from the Ampliconnoise folder and if a similar issue raised, proceed in the same manner.

Success with the ApliconNoise after repairing several makefile.

The addon TopiaryExplorer installation instructions were likewise tough to trackdown. They are at

-To be continued


Directing your computer to use DropBox for your Document folder

To conserve disk or SSD storage space and time, you can save files directly to Dropbox from your computer programs that want to save to your Documents folder. This requires simple commands in Terminal for Mac OS or a small settings change for Windows.

For Mac OS, open Terminal (in Utilities) and type cd Dropbox. Press enter, and then type ln -s ~/Documents /Documents. Hit enter again to complete the process.

To segregate the Document folder of multiple users, or home machine from work machine.

To be clear you can use any file under the Dropbox folder if you want to segregate your work machine from your home machine. Just add the folder you want to use as the target under Dropbox.

To save the Document folder from a two different Mac machines as above type cd Dropbox at the command line in Terminal on the home Mac. At the terminal type mkdir HomeDocuments. Then type ln -s ˜/Documents /HomeDocuments. Hit enter to complete the process. The form of this symbolic link command (ln -s) is source directory followed by target directory.

If you do not want this HomeDocuments folder, sub-folders, and included files showing up on your work Mac you will have to use Selective Sync on your other Mac and uncheck the HomeDocuments folder. This process can be repeated from a work Mac using a different folder name (WorkDocuments).

The use of symbolic link (ln -s) can be handy as the user can even choose subfolders in the Documents folder and send files to Dropbox while leaving other subfolders resident on the machine without linking. One word of warning is that moving the source breaks the link.

It is more cumbersome on Windows machines and the granularity is less elegant. In Windows, right-click on your My Documents folder, hit Properties and click Move. Then select your Dropbox folder.

Viewing hidden files in OSX Finder

To view hidden files in Finder go to the Spotlight and enter Terminal. The Terminal app should be the first choice.

Start Terminal and at the command prompt enter:

defaults write AppleShowAllFiles -boolean true
killall Finder

Now when you return to Finder the lighter grey file names are files that are normally hidden and are now visible. Generally, it is not prudent to delete these files unless you have investigated the implications of deleting these files.

The difficulty now is that thereafter the hidden files will show in the Finder. To make the files hidden to the finder again, enter the following at the command prompt in Terminal:

defaults delete AppleShowAllFiles
killall Finder

While this is a bit techie, I do have need of this from time to time. Mostly, in user mode, we don’t want to be bothered with seeing these files.

However, sometimes I am communicating with users who live in the Microsoft Windows Operating System world and they are confused when they see hidden files in shared folders. This is especially true of some of the shared cloud folders for collaborations. It those cases, I can sometimes simple state that the files preceded by a ‘dot’ are to be left alone.

Sometimes, I must go further to satisfy their curiosity, or to convince them to leave those files alone, and then I explain that the prepending ‘dot’ hides the files in the BSD, UNIX, and LINIX operating systems. Generally, I don’t have to go farther than that, but occasionally, it helps to point out specific examples and to name a file that they are seeing in there ‘explorer’ that is/are to be left alone.

Perhaps the quickest way for me to see the hidden files to point out an existing example file they are seeing, is to enter the Terminal app and list the folder in question using the command

[Machine_Name]:[Path_to_Folder] [User_Name]$ ls -al

Where I have navigated to the folder [Path_to_Folder] in question.

I have found that when we are looking at the screen of my Mac together, the Windows user can be severely intimidated by the command line. They seem to simply stop processing anything that is said when the terminal is open. Not their fault! They might have never seen the power and majesty of the way computers really work (and they probably never saw the first Tron movie either).

Therefore, the above method of revealing the hidden files in the Mac OSX Finder has, in my experience, been a ‘less jarring’ experience for them.
Though you might have to envok a little ‘wizard of OZ “pay no attention to the man behind the curtain” while you run the command to reveal the hidden files. (Hint: you can have a stickie that has the command at the ready to paste in at the command line)

Do you have a favorite Apple Mac OS X terminal command?

Screencasting and Retina Screen Resolution

The early 2013 MacBook Pro 15 inch Retina display I have been using lately has an incredible amount of resolution. However, when I recently went to make a screencast with this machine I realized that all this beautiful resolution makes for poor looking screencasts.

While this post discusses the MacBook Pro and its Retina display the concepts are applicable to any hardware and operating system: think Microsoft Windows here.

On this Apple OS-X operating system, I mostly use three applications to capture the screencast: Camtasia, Screenflow, and Quicktime. The folks at Telestream make Screenflow and they have a quite good blog on choosing the best screen resolution for screencasts if you want more, but before you click through to that blog let me explain the background a little below.

If the target audience for the screencast has the same Retina resolution, and they wish to view the screencast full screen, then my “poor looking screencasts” statement is false. If the source and target are not equivalent and the target is smaller; then that  statement in the first paragraph of this post is correct.

I can scale the export to a smaller resolution. Perhaps you have seen the fuzzy and/or tiny fonts in screencasts and have also been disappointed with the quality of the experience. Turns out those words and fonts in screencasts are really hard for the video capture programs and scaling them down makes for a poor product.

Size of the file is also an issue for my target audience. I am a University Professor delivering a fair amount of the screencasts I produce via our Universities Learning Management System (LMS) BlackBoard. I upload the files to a server and the student watches them, ideally, from within the BlackBoard Content or Learning Module portals. Lots of bandwidth is used in this round trip.

The quality of the text on the screen is hugely important to the majority of my screencasts. I certainly desire to avoid muddling the learning concept I have in mind with poor quality text and visuals.

When I recently created a screencast the Screenflow the canvas was 2500 x 1600! When I tried to scale the screencast down to 1280 x 800 as I exported it, the result was less clear than I wanted.

I thought easy enough to change the resolution on the MacBook, but I was stymied. I went to System -> Preferences and choose the Displays widget I was presented with choices for scaled resolution. However, when I choose a “Larger Text” resolution and rerecorded the canvas size was still 2500 x 1600.

While I am sure I could learn to use the command line to accomplish a true screen resolution change in Display, I thought that was not a viable fix for my workflow. Instead I found a Mac OS X utility to help from Stephane Madray. This shareware program is called SwitchResX.

Now I can change the resolution to something more reasonable prior to recording. When exported to the delivery format has less, or no, scaling of the screen size then I will achieve the clearest video with the smallest file size.

ClamXav Sentry setup

“ClamXav is a free virus checker for Mac OS X. It uses the tried, tested and very popular ClamAV open source antivirus engine as a back end.”

ClamXav is a free virus checker for Mac OS X.  It is located at  Though viruses attacking OS X users is none, it is kind to scan email that may be replied to Windows users.

I am running ClamXav-Sentry to scan download folders and email folders.  The user must add the folders that ClamXav-Sentry watches and at first I added


~/Library/Mail Downloads






These folders have all subfolders scanned also.

But every time the mail program checked my nine (9) email accounts I had many dialog screens filling my desktop each alerting me that a single email had been identified with a virus and had been quarantined.  Wow every day their were dozens likely owing to the long length of time I have had some of these accounts. I do not see a way to turn these notifications off.

This was a little frustrating.  Then it occurred to me that the mail servers were already shunting infected emails to spam/trash/junk folders and that I was rescanning these.

My solution is to not scan the mail folder and all subdirectories with ClamXav-Sentry, but to scan the Inbox for each account.

So, ~/Library/Mail  is removed and a list of ~/Library/Mail/xxxxxxxxx/INBOX.imapmbox

The comprehensive scan will catch the emails in the spam/trash/junk folders of each account when it is evoked.

A final piece of the setup is that to see the Mail folder in Library you use the column view.

Presentation Software

I have to admit I am starting to develop bad habits.  I know better.  I have to be stronger at resisting.

“PowerPoint makes us stupid.”
— Gen. James N. Mattis, Marine Corps

I came across this page.

What Not To Do When Making a Keynote Presentation

by Dr. Donald E. Wetmore

In academia we are constantly pushed to take important information and make it simple.

I like steak.  If someone chops up a steak and then puts it in a blender until I no longer have to chew, it is just not the same!  This is what students often ask for.  Furthermore, they want us to add sugar.  That’s baby food!  In college, students need to chew on it.

Don’t get me wrong.  It is important that the steak is cooked correctly; and the cut of meat determines the preparation, cooking, and presentation of the steak.

Presentation is important, and Dr. Wetmore has a few Don’ts that I agree with.

Podcasting or Vodcasting

I have begun to explore the world of podcasting.
During a recent presentation at a Universal Design Faculty Learning Community Committee meeting at Tarleton State University I was asked about the hardware, software, and work flow for the creation of a rough Enhanced Podcast that I produced and demonstrated based on a lecture module for my Soils, Land Use and The Environment (AGRN302) course.

The Enhanced Podcast was audio laid over the Powerpoint(R) slides.  I used on my MacBook Pro to do this.  A very nice feature was the addition of loops.  Apple has a very brief how-to.

plantronicsFoldingThe Plantronics headset (Plantronics Foldable USB Stereo Headset) was chosen after a, not inconsiderable, investigation on the web.  I believe what swayed my decision to purchase this headset was several comments to the effect that if the podcast creation task was untenable that the headset could be used for Skype or music.  The price was modest and the audio is acceptable.  I have noted that the audio can be different from on session to another so I must be mindful of this.


Suppress all but errors

If computers get too powerful, we can organize them into a committee — that will do them in.” —Bradley’s Bromide

I’m too cheep to buy a program to do backups and file synchronizations to USB drives.  Using MS Windows I purchased a program called ‘Synchronize It!’ that was really wonderful to use.  Coming back to Mac after being away since my Mac Classic I looked for a replacement to ‘Synchronize It!.’

I gave up looking right away because I knew that UNIX machines have this built in at the command prompt level.  With my MAC I just fire up Terminal and evoke rsync.

While rsync is undoubtedly considerably more powerful than Synchronize It!, I was less familiar with it.  Oh, I’ve used it on LINUX, but hardly could I say that I was familiar or comfortable with rsync.

I’ve been running the following:

sudo rsync -au --progress --human-readable --prune-empty-dirs /source/path/ /dest/path

This gives lots of output on the terminal window, but can be tiresome.  I wanted to suppress the output of all but the errors.

I tried:

sudo rsync -a --update --prune-empty-dirs --quiet

rsync: delete_file: rmdir “a directory” failed: Directory not empty (66)

rsync error: some files could not be transferred (code 23) at /SourceCache/rsync/rsync-35.2/rsync/main.c(992) [sender=2.6.9]

I do not see the error directories or files for the second error.

To test things out a little I added –list-only switch.

Still I wish to see the files that were not transfered.

Conclusion = pending.