All posts by DonaldMcGahan

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 http://www.mitchchn.me/2014/os-x-terminal/ ]

Arthur Gareginyan at mycypberuniverse.com has an explanation of how to use the ‘find’ with terminal to identify zero sized (empty) files and folders. [ Last Accessed July 29, 2016 http://mycyberuniverse.com/linux/find-and-delete-the-zero-size-files-and-empty-directories.html ]

Mike Rubel has an article at [ Last Accessed July 29, 2016 http://www.mikerubel.org/computers/rsync_snapshots/index.html ] 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).

CommandLineFU.com has a commendable repository [Last accessed August 2, 2016 http://www.commandlinefu.com/commands/view/10039/find-duplicate-files-based-on-md5-hash-for-mac-os-x ] 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 rud.is 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
 
# OR YOU CAN DO
 
brew cask install basictex # suggested by @noamross
 
# DO NOT DO BOTH!
 
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

Update.

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

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

That’s it.

Citations, blog posts, and WordPress

When adding citations to blog posts the bibliography as an endnote seems untenable. The very nature of web pages promotes a non-linear approach to content.

Browser tabs help quickly switching between pages, but the reader has to get to the page with the endnotes (bibliography). It is annoying to know the author is referring to a scholarly work, a clarification, or another web page and not have a ready hyperlink to what is referred to.

Bloggs and web pages are actually fairly straightforward links to add in WordPress. If either of these are from you’r own site it is relatively easy, if you’re good at the page or post titles.

Academic writing frequently uses inline citations and Reference lists  or Bibliographies at the end of Articles. Books are another story. When a book has multiple authors and compiled by editors each Chapter is self contained with respect to the inline citations and bibliography or reference list. It would not be uncommon to direct a citation back to a specific Chapter.

Increasingly, Books, and Book Chapters are available online.

This weblog post chronicles a glimpse of my approaching citations to Books and Book Chapters using WordPress in the least cumbersome and most coherent manor. I would like my site to have some coherency and reflect scholarly norms by including citations. Wikipedia is also moving down this path of documenting the citations on a per-page basis.

Another issue is that I reuse Book and Book Chapter citations and it would be handy to have them ready made in WordPress similar to how pictures. Another example that I have found is the TablePress plugin for reusing tables.

Where I am at

The current list of webpages that I am looking at to help with this is below.

Limited time keeps me from attacking this in one chunk. I expect this list to grow and this post get refreshed and updated.

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.

Scaling iPad photos for use in presentations or weblogs

Images are a great way to engage an audience.  A quick look on Wikipedia for the phrase “A picture is worth a thousand words” will return the premise of the use of graphics, be they drawings or photographs.

Binging pictures into a PowerPoint, Keynote, or Prezi presentation is easy enough. Pictures we take today with our digital cameras often contain much more resolution, and are much larger in file size, that is necessary for projecting during a lecture. Even the cameras in todays tablets and phones are overkill for projected images.

Large images take up space on storage media, are slower for the program to load, and if the presentation is located in the cloud, requires significantly more bandwidth to transfer.

Scaling images is a “best practice” for matching a presentations content to presentation delivery method.

Beyond the face-to-face presentation software, digital delivery to distance learners also has similar constraints with the bandwidth to transfer to the end user increasing in importance in the consideration of image quality and file size.

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/Emacs.app/Contents/MacOS/Emacs -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.

/usr/bin/rsync

 

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 http://clang.debian.net/status.php?version=2.9&key=FUNCTION_RETURNS_VALUE

This may be related to Xcode so I went to https://developer.apple.com 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 http://topiaryexplorer.sourceforge.net/user_guide/install.html

-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.

Why carry the iPad in addition to MacBook Air for Travel

Why carry an iPad and a MacBook Air (or any laptop)?

Well beyond the stellar battery life and more comfortable form of the iPad in those crowded airliner seats, when your watching that move or training video, there are justifiable reasons once you leave the airliner. Enter the iPad Google Docs app and Google Sheets app.

Air
Air
iPad
iPad

Continue reading Why carry the iPad in addition to MacBook Air for Travel

Google Docs and Sheets Advantage

The Google Docs and Google Sheets Advantage

Google Docs and Sheets are handy when collaboration is likely to benefit from a parallel rather than serial workflow. They have a distinct advantage over cloud hosted documents accessed by applications that create copies when multiple users edit and comment simultaneously.

1403465406_google_docs
Google Docs Icon
GoogleSheetsIcon
Google Sheets Icon

 

Such “conflicted copies” must be reconciled into a master document at some point and this has previously be a chore. Emailing a Microsoft Word or Excel document, or similar formats created with alternate program, to collaborators has long been a viable way to collaborate. However, I have noted that as the number of collaborators increased the management became more and more of a chore.

I have noted a severe avoidance behavior in collaborations where a chair of the collaboration, in a desperate bid to avoid reconciling multiple documents, decrees that the document will be send from one collaborator to another in a serial fashion. While handing the document from on collaborator to another, like a baton in a relay race, does decrease some of the management workload (the manager does not have to evoke MS Word Merge Documents function), it really stifles interplay and collaboration between early contributions and later contributions. This serial collaboration works in some documents but a more parallel collaboration should produce a richer final product.

Beyond the richer final product that can be achieved with parallel collaborations, two other advantages are achieved. First, the “when the iron is hot” advantage. Frequently, time is a limitation for all the collaborators. Having the document available to all the collaborators from the inception through to completion increases participation. Second, because the interplay of ideas and contributions is more free between collaborators there is room for adjustment of the presentation of ideas. It is the latter of these two that might be one of the most powerful.

In another post (Google Sheets, Docs, and Forms are Failures for Traveling) I blogged how I found Google Docs and Sheets to be a failure for my purpose. In that post I was describing the access to the document from my Ultrabook laptop computer.

In another post I describe how carrying an iPad with the Google Docs and Google Sheets app installed may cause me to carry both my  my iPad in addition to my MacBook Air.

Google Sheets, Docs, and Forms are Failures for Traveling

Why Google Docs, Sheets and Forms are not the ‘Best’ solution.

Recently I attempted to use Google Documents in support of a Study Abroad University course.

First, why I wished to embrace Google Documents?

Google Docs Icon
Google Docs Icon

The Study Abroad Course that I tried to use Google Documents with was taught by myself and another professor.  We needed access to logistic information and often this collaboratory effort(s) happened in intense sessions where we were accessing or creating information real time and sometimes at the same time. Additionally, we had support staff that, at times, needed to contribute and access the information.

What worked

We found Google Docs and Sheets to be very useful in the academic setting while planning and preparing the course logistics. This is a real strength for Docs and Sheets. At no time were we unable to access the information, and the realtime nature of Sheets and Docs was gratifying. We even set up Forms to leverage recording information from students in a Sheets.

What did not work

Access to Sheets and Docs once I was traveling abroad was abysmal. It is not as if I was traveling to a country without robust internet infrastructure. I was traveling from the USA to the United Kingdom, primarily London Heathrow Airport, and then on to Poland, Warsaw, Krakow, Bydgoszcz, and Gdansk.

Access to Google Sheets and Docs requires access to the internet. Obviously when traveling abroad 3G, 4G, LTE cellular access is possible, but very expensive. While wifi locations are daily plentiful in Poland, the Google experience was frequently, and I do mean frequently, uninspiring. While access to DropBox, and iCloud documents was nearly flawless, Google drive Docs and Google Sheets was not. Furthermore, even when Google Drive reported that the documents were in-sync starting Sheets or Docs frequently failed, or terminally stalled, when trying to load the documents. These documents were not particularly long, complicated or large in size, so this was very frustrating.

My experience with Google Sheets and Docs was good when sitting at my desk with a fat internet pipeline of the academic setting. It was also very transparent from my home DSL broadband. However, once I moved away from this fat pipeline to the internet of hotel rooms and wifi cafes, these medium to slow access speeds, or increased latency of some of the wifi (and obviously 3G, 4G and LTE) locations, the experience was miserable, frustrating, and left me with a great desire to move away from this Google product and find another for future endeavors of this sort.

As stated, I found that DropBox and iCloud worked acceptably while traveling. DropBox and iCloud are not as slick when sitting at my desk at my home academic institution. Why? They do not offer the experience with respect to realtime editing and collaborations.

Is there something else?

Perhaps, but probably not principally different from the above named products. Worth noting is that I have not used the Microsoft product at this time, mostly because of some very acrid opinions of many of my colleagues about that product. Interestingly academic administrators like the Microsoft product much more than those of us ‘in the trenches’ of creating long, diverse, and sometimes complicated documents for publications and presentations.

Regardless of the products that are available, we must consider all of our users. We Americans are so forgetful that most of the world does not have the connectivity that we enjoy on the American University Campus. We exclude the disadvantaged in our rush to embrace the latest, and most cutting edge, tools. I am guilty of this as evidenced by my chronicling this experience.

Is Google Docs and Sheets a tool for today.

No. So far it is elitist. It is for the well connected user who will always have that ‘connection’ that is robust and clutter free. If it were the tool for today then Google Chrombooks would be taking the world by storm. They are, after all, cheaper than a device that does not require a constant connection to the internet to function acceptably.

Verdict

Not again soon. I would really like to see this product succeed. However, for today it needs a fall back local copy to be truly useful for the use by the masses. Otherwise, it is elitist. Reserved for the rich in data transfer speed and low latency.


Post Script see the posts Google Docs and Sheets Advantage and Why carry the iPad in addition to MacBook Air for Travel

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 http://www.clamxav.com/index.php.  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

~/Library/Mail Downloads

~/Downloads

~/Public

~/Sites

~Users/Shared

 

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 GarageBand.app 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.

SOILWEB for the iPhone

A new soil iPhone application is available on the iTunes store.

http://itunes.apple.com/us/app/soilweb-for-the-iphone/id354911787?mt=8

SoilWeb

SoilWeb for the iPhone        By CA Soil Resource Lab

The principal author is Dylan Beaudette.

At the SSSA meetings Pittsburgh. PA. 2009 Annual Meetings, Nov. 1-5, Pittsburgh, PA I had a chance to visit with Dylan Beaudette and catch up on his pedological escapades.  At that time I suggested that he write an iPhone application as an extension of the Online Soil Survey he wrote so us soil-heads that use an iPhone could walk around with SURGO data in our shirt pocket!  He has done it.  It started out with AZ, Ca, NV, & OR and at my request he has added Texas. He is now in the process of  adding NM, CO, UT, & WY.

Who needs a pocket protector when you have a shinny iPhone! 🙂

Yes, I love the paper copy of a Soil Survey, but I often am caught without a copy in my back pocket.

I have tested this app in its development forms and it’s great.  It’s FREE.

Dylan is a doctoral candidate at University of California, Davis.  Dylan’s mentor/advisor is Dr. Anthony ‘Toby’ O’Geen.  To see other things that Toby’s group is working on visit http://casoilresource.lawr.ucdavis.edu/drupal/

Soil as battery

Soil and technology. So much technology comes from our exploration, and mining, the soil for its goodness.

I was snooping around the web and ran across a post by Carl Alvin at Core77  titled “The amazing dirt-powered lamp” posted September 30, 2008.

I have taught soil laboratories and done demonstrations where we used a clay suspension, think of a clay mud bath that is a little to runny, to power a small light bulb. Just takes a copper wire and a zinc electrode separated in a beaker of the suspension.

It is a curiosity to some but it helps to link together the concepts of bacterial electron transport chains in their cell wall, electron movement in soil, and electron movement to power lights and do other work.

Learning Differences

Morpheus: ‘I’m trying to free your mind, Neo. But I can only show you the door. You’re the one who must walk through it’ —The Matrix (Film)

About a month ago I was pondering how I might deliver lecture content in ways that might address learning differences.  I came across a YouTube presentation that appealed to my scientific training.  The presentation was by a Professor Daniel Willingham who is a cognitive psychologist at the University of Viriginia.

What I took away from this video is that no tests have been devised that can distinguish differences in learning. I personally believe that their are learning differences and until it can be proven scientifically I have to acknowledge that my belief is based on personal experience and on faith.

I would suggest that the population they have used in these studies is representative of our population in general. I wonder if anyone has tried to use learning disabled students as a population to differentiate these differences.

Daniel produced a clarification that mollifies some of the conflict.

http://www.youtube.com/user/dbw8m#p/u/4/vdJ7JW0LgVs

rsync

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.