ademcan's blog

Installing RStudio Server on Mac OS X Lion

14/04/2013 - 2 comments

    RStudio is a great IDE for the R programming language. Two versions of RStudio are available, the desktop and the server edition. The desktop edition is a full version running locally and the server edition is running on a server with the graphical RStudio interface accessible from your web browser. At work I am using a Mac Pro as a personal server with all my data and my running scripts. To preserve my memory (RAM) on my laptop I wanted to run R from my server. Until now, I used the command line with ssh, but after testing RStudio I couldn't go back anymore :)
    You can install RStudio Server in any machine and access its graphical interface from any web browser. You will then access your normal IDE running R (on the server-side) with your Rhistory and R plots remaining there.
    Recently, I found the following tutorial about how to install RStudio server on Mac OS X Lion. It works very well, but I got an error at some point. After running the following command

sudo ./install-boost

I got an error claiming that bootstrap.sh was not found. To continue the installation, you need to run bootstrap.sh by yourself. To do so, run the following commands from your terminal

cd $YOUR_RSTUDIO_INSTALLATION_FOLDER/dependencies/common/boost-build/boost_1_50_0
sudo ./bootstrap.sh
sudo ./bjam --prefix=/opt/rstudio-tools/boost/boost_1_50_0 toolset=clang variant=release threading=multi link=static install

Of course, change the version of boost if your are using a more recent one. Don't forget to modify $YOUR_RSTUDIO_INSTALLATION_FOLDER by your Rstudio installation folder path.
Then, continue with the normal installation process, everything should go well.
Browse to http://localhost:8787 login with your username and password you use for the computer where you installed RStudio server and enjoy ;)

image: rstudio.org

UPDATE: Opera is not supported by RStudio BUT works with IE if you install the Google Chrome Frame plugin. OMG :)

Tags : HowTo, Mac, Server, Software

Add tabulations in your articles with Blogotext

07/04/2013 - No comments

I am using Blogotext as blog engine. It is a big pleasure to use it :) Blogotext is open-source, easy-to-use and very light, it works very well. I would like to thank again Timo for his great job.
I am using paragraphs to organize my articles and make them clearer. In addition, I like to start each paragraph with a tabulation. Unfortunately, it is not easy to add tabulations using the default Blogotext editor. However, you can do it by forcing 4 spaces, such as

&nbsp;&nbsp;&nbsp;&nbsp;

I wanted to make it easier, thus I decided to implement this option in my editor.
The default Blogotext editor's menu looks like :

After implementing the tabulation option, you'll see an "indent" icon in the right-hand side of the "line-through" icon :

To do so, you will have to modify two lines in two different files:

1 - First,

open the file /admin/form.php
go to line 581

add

echo "\t".'<button id="button15" class="but" type="button" title="tab" onclick="insertTag(\'\&nb\s\p\;\&nb\s\p\;\&nb\s\p\;\&nb\s\p\;\',\'\',\'contenu\');"><span class="c"></span></button>'."\n";

2 - Second,

open the file /admin/style/style-ecrire.css
go to line 184

add

#button15 span.c { background-image: url("format-bbcode/edit-indent.png"); }

If you want, you can modify the icon by choosing another one from your /admin/style/format-bbcode/ folder.
Enjoy ;)

Tags : HowTo, Software, tips

HyperSwitch, an interesting app switcher alternative for Mac

06/04/2013 - 4 comments

    The default app switcher on Mac (cmd+tab) doesn't show the different opened windows for a given application. For example if you have multiple LibreOffice windows opened, you will only see one LibreOffice icon on the app switcher. I think this is a great productivity-killer :)
    When I was looking for an alternative, I first found Witch. Witch looks promising but it was too complicated for me. I also didn't like the vertical presentation of the app switcher.
    I then managed (I don't know how) to find Senebier :) I just don't understand what's written and didn't read any positive or negative comment about this app. I didn't installed it yet, but I contacted the author to ask if the source code will be available at any time or not.
    Finally, when following my feeds from LifeHacker, I stumbled upon an article about HyperSwitch. This app switcher is still in Beta but it actually works pretty well. Once you started the app switcher and moved to an app icon, you can:

press the down arrow to you see all the open windows and switch to one of them
press the up arrow to open a new window for that app or see the most recent files

I am actually giving a try to HyperSwitch. It is a promising project, still in beta, but I am sure it will improve a lot very soon.

Source : HyperSwitch website
LifeHacker's article about HyperSwitch
Image : RoaringApps

Tags : Mac, Software

Leed: your web-based open source RSS reader

03/04/2013 - 2 comments

    As you can see from my older posts, I am becoming more and more self-hosted every day :) I already have some interesting services running on my own server, don't worry I will write about all of them. Last time I wrote about Shaarli, a great and open source links managing tool. Today, I will introduce you to Leed (for Light Feed). Leed is an open source RSS reader alternative to Tiny Tiny RSS or RSS Lounge for example (and the almost dead Google Reader). I never tried any RSS readers before, I was mainly reading my feeds in Thunderbird, thus I cannot compare Leed to its existing alternatives. I can only say that Leed is great.

    I wanted a web-based RSS reader to access my feeds from any devices everywhere. I recently discovered Idleman's blog (in French) when he started his tutorials about the Raspberry Pi. Then I found his project's page and Leed.
Leed is an open source and light RSS feed reader. The installation is very easy.
The "only" requirements are:
- Apache server
- PHP 5.3
- MySQL

    Once installed, you can use crontab to automatically update your feeds, or you can do it manually if you don't want to deal with crontab. You can use keyboard shortcuts and personalize the interface using themes. You can easily implement your own themes. The default theme is responsive, thus you have an easy access and user-friendly interface in any of your devices (tablet, smartphone...).
One other great option is the link between Leed and Shaarli. If you are using Shaarli, you can automatically add any articles from your feeds to your Shaarli.
Leed is very simple and Leed works :)

When I was writing this post, I realized that Leed was only available in French. After asking the permission to the author (Idleman), I translated Leed and the installation process to English.

How to install Leed:
1 - Download the archive LeedEnglish.zip (Licence : CC by nc sa)
2 - Unzip and send the content to your server. Do a chmod 777 to the leed folder
3 - Go to the installation page http://mydomain.com/leed/install.php and follow the instructions
4 - Once the installation is finished, remove the install.php file for your security
5 - If you want to update automatically your feeds, put the following line into your crontab
Open crontab

sudo crontab -e

and add the following line for an hourly update :

0 * * * * wget -q -O /var/www/leed/logsCron "http://mydomain.com/leed/action.php?action=synchronize&code=your_synchronisation_code"

(adjust the link and your synchronisation code)
Be warn that too frequent updates can slow down the server.

Don't hesitate to ask if you have any question or remark ;)

A demo of Leed is available online here

Tags : Server, Software

spliceIt available for iOS and Android

01/02/2013 - 3 comments

I recently finished my first augmented reality (AR) app: spliceIt. This app contains some of the results about alternative splicing regulation I obtained during the first two years of my PhD. It also contains a 3D representation of the spliceosome using AR.
To see the AR 3D spliceosome, go to the "Spliceosome" menu and focus your camera to the picture of the shiny spliceosome. You can pinch to zoom and slide to rotate the 3D spliceosome.

spliceIt on the Google Play Store

spliceIt on the iOS Appstore

Feel free to use it. I am looking forward to read your comments.

Tags : Software

Share your links with Shaarli

08/01/2013 - No comments

I recently installed a new tool on my server at home: Shaarli. Shaarli is a very light open-source clone of delicious. You can use it for many different things: share your links, save your bookmarks, use it as a notepad, share text or information easily among your different devices...

Why is Shaarly great:

add all your links with a specific tag
find your links by tag or keywords
draw a tag cloud to see the most commonly used tags
add a bookmark on your browser to automatically save new links
see all your images using the picture wall
generate automatically a newspaper-like page containing all your daily links
... more features on Shaarli's official webpage

I installed Shaarli a few months ago and I am using it very often as a bookmark accessible from everywhere, any device, any web-browser, simply great.
Shaarli requires php 5.1 (5.2 for autocomplete).
You can find an example at http://sebsauvage.net/links/
I will keep posting about interesting tools/services for self-hosting cool

Tags : Server, Software

Distribute your iOS app OTA with HockeyKit

21/12/2012 - No comments

     Recently, I started developing for iOS. It is a very interesting platform and a very good experience for any developer. I like working on iOS, but the most painfull part of it is the distribution of your application. With Android, you can distribute your application file (.apk extension) everywhere and everybody can download and install it easily. In contrary, with iOS you have to sign your application and can distribute it only througth the AppStore. This is very problematic when you want to distribute your application for beta-testing. Actually, you can test your application in 100 iOS devices if you have a normal (not enterprise) iOS developer account. You need to add in your account the unique identifier (UDID) of all the devices you want to use for testing and send them a provisioning profile, which allow the device to run applications signed using your Apple developer certificate.
     While coding my first application, I wanted one of my friend to test it. The first thing I did was to generate the .ipa (the application) file from Xcode and send him an email containing the .ipa and the .mobileprovision file. Then, my friend had to use iTunes to synchronize these two files with his device. This is not the best option for both the developer and the tester. The developer will have to send an email (or use FTP) for each version of the application and the tester will have to sync with iTunes each new version of the application he receives. Luckily, I read somewhere that from iOS 4, Apple allows the over the air (OTA) distribution of .ipa and .mobileprovision files. While searching for more information on DuckDuckGo, I found HockeyKit.
HockeyKit is a solution for iOS/Android application OTA distribution and is the best option for the developer and the beta testers.
     You can install HockeyKit on your server and use it as an internal app store. You only need PHP5 installed on your server. HockeyKit will generate a webpage containing all your app and allow testers to install your app on their devices directly from Safari. You can use HockeyKit for many application with many different versions. The testers devices have to be added in your account and you need to provide the .mobilprovision file in your HockeyKit installation. Basically, you need to load three files for each project:

the .ipa file which represents the application itself
the info.plist file containing different information about your application such as the name and the version
the .mobileprovision file containing the information about the devices that can install your applications

Any time you have a new version of your app, you can upload it to your HockeyKit server and let your beta-testers know that they can install it.
HockeyKit automatically generates the webpage presenting all your projects with the summary of the content, and the changes from the previous versions. If you want to go further, a client version of HockeyKit is also available. Once installed on the tester device, any new version will be announced automatically, and you can obtain direct information about the usage and statistics for your app. It is very easy to use, I can highly recommend it.
Of course HockeyKit is open source ;) and works fine with Android as well.

Tags : Software, tips

SolEol: Automatic search and download of movie subtitles

19/05/2012 - No comments

     I recently found a very interesting tool: SolEol. This tool will help you in finding subtitles for your movies. You simply need to "Drag and Drop" your movie file in the appropriate window in SolEol and it will search the internet for the subtitles in any language. This tool uses the subtitles from the very good OpenSubtitles project.
     In the Menu, you can define your preferred subtitles languages, choose the option "Rename Subtitles as Movie" to show directly the subtitles when the movie starts and also save your username and password if you have an OpenSubtitles account.
     I cannot say more about this tool as the communication (on their Twitter and in some parts of the website) is mostly in Spanish smile

but the project seems very active and new features such as video format conversion will be coming soon.

SolEol is available for Linux, Windows, Mac and even PPC Mac and is under Creative Commons Licence.

Tags : Software

hubiC: your secure hub in the cloud

14/05/2012 - No comments

     OVH is a french hosting and internet solution provider. Actually this blog is hosted by OVH. Few months ago, OVH released their new project hubiC (hub in the Cloud). This project is similar to DropBox, iCloud or very recently Google Drive. I didn't tried these cloud storing services thus I cannot compare them, but I really like hubiC.
     With hubiC you have 25 Go of storage place for free. If you want more space you can choose other options: 9.90 €/year for 100 Go and 69.90 €/year for unlimited space. You can save everything you want and access it from everywhere with an internet access. To create an account you simply need to register with a username and password. Different tools exist for accessing your hubiC storage place from almost all the mobile and desktop operating systems.
     I recently tried the iPad version of hubiC. After your login you access your folders, you can create or delete folders from this app. The iPad version contains an image and pdf readers to see your files contents.
     I also like the secure part of hubiC. Nobody can access or check your files, you are the only owner of all the data you have in your hubiC. You can upload any type of file (pdf, doc, jpg, wav...) up to 10Go. A sharing option is available on hubiC: by simply clicking the “share” button, you obtain a link that you can send to people you want to give access to a given file or folder in your hubiC. For now, most of the hubiC tools are in beta but the project is growing very fast and new options such as online file editing or private sharing will be added soon.
     If you want to give a try, you can have a look here (only in French).

Tags : Software

Owncloud: your personal open-source cloud

23/03/2012 - No comments

     We are actually living in the cloud generation, and nobody can ignore it. You don't have to be a geek to understand what cloud computing means, because we are all directly or indirectly using cloud-computing services. Cloud-computing means the usage of a global machine (for storage or computation) rather than your local machine. We can cite iCloud, Dropbox or SkyDrive within many other cloud services for data sharing. With cloud computing you have access to everything (files, calendars, contacts, music, pictures...) in your cloud from everywhere with the only condition to have an internet connection. With the new generation of cellular data (3G), the rapidly developing 4G and many different free WiFi hot-spots, internet access is not a problem nowadays.
     In my case, I was using iCloud as a cloud-computing provider mainly because of my Apple-based environment (MacBook as laptop and iPhone as smartphone). I had all my calendars, contacts, reminders and iPhone backups data on iCloud and could access everything from my phone and my laptop. The only point I didn't like with iCloud and other cloud services is to be dependent from someone. If one day iCloud decide to close or change its privacy policy (see Google recently), I won't have my word to say. I prefer to use open-source and multi-platform tools when possible. I recently discovered Owncloud, which feets very well with my philosophy.
     Owncloud is an open-source alternative to all the cloud-computing or service providers. Once Owncloud is installed on a server, you can save all your data, calendars, contacts, music... and access everything from your computer or cell-phone using any web-browser. Owncloud is very easy to install and has a lot of very interesting features. The graphical user interface is beautiful. All the protocols used in Owncloud are very common and widely spreaded protocols such as webDav for file sharing, calDav for the calendars and cardDav for the address book. You can find a lot of different tools that support these protocols for all the existing computer or mobile platforms.
Owncloud integrates a PDF reader and a text editor function. The text editor can recognize many different programming languages and highlight the code you are writing. A music player is also available on Owncloud, after uploading your albums in Owncloud you can listen all your music within any web-browser without any additional tool

     Why I like Owncloud ?
     I am using a lot the calendars and contacts on my laptop and my phone, it is just a pleasure. It works very well on iPhone and Thunderbird. I am not limited on the disk space as I installed Owncloud on my own server. I am the only person with access to my data, but I can also give limited access to other people for some specific files for example. I can always modify or add a new function to Owncloud very easily with some basic programming knowledge.
     The actual version is number 3 and the version 4 is already on its way with some new features planned such as a Notes application and even an email provider. The community is growing every day and the forum is full of people willing to help for any question and open to remarks and suggestions. You can even propose your own application to the Owncloud community using their app database.

Last but not least, you can try Owncloud without any installation here.

Tags : Software