solving DESeq2 installation issues

At work a colleague asked me to do a system-wide installation of the R module DESeq2 in one of our internal servers.
The installation procedure is quite straight-forward:

source("http://bioconductor.org/biocLite.R")
biocLite("DESeq2")

Unfortunately I had some issues on my system, in fact I got:

…
Warning in fun(libname, pkgname) :
couldn't connect to display "localhost:12.0"
* DONE (maSigPro)

The downloaded source packages are in
	‘/tmp/RtmpfdD2RC/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘annotate’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘genefilter’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq2’ had non-zero exit status

I then tried to install manually the various dependencies, like XML. Still no luck. After a quick Google search I found that I was missing a couple of -dev packages on my Ubuntu machine, so I installed them:

root@server:~# apt-get install libcurl4-openssl-dev libxml2-dev

… and then re-tried to install DESeq2. This time everything was ok. Problem solved!

RightFont, helping designer getting the right font

RightFont for Mac is a brand new app, currently in a public beta testing program aimed to help designers in choosing the right font for their project right inside their favorite application.
At the moment the app work seamlessly with Sketch and Adobe Photoshop, with Illustrator and InDesign coming in… Give it a look!

Momentum, the Google Chrome app everybody asks me for

Momentum on Google Chrome

I can’t actually say when or where I first read about this Momentum thing for the first time. Fact is that since I’ve encountered it, this Google Chrome extension has caught my eye and I’ve installed it straightforwardly.

Each time I open a new tab in my browser – and you know that it happens dozen times a day – I’m being welcomed with a gorgeous and inspiring image. I’m remembered what the most important thing I have / want to do in the day so to focus on it.

As corollary I can set a short to do list (below on the right), have a look at the current external temperature (above, right) and be rewarded with a meaningful quote (on the bottom).

Momentum →

Momentum is a personal dashboard designed to eliminate distraction and provide inspiration, focus, and productivity.

I have to say that this extension has a benefic and relaxing influence to me. It’s a quick glimpse of real world beauty, opposed to the artificial and cold one of a computer screen. When I’m using other browser I do actually miss this “moment of peace” … and I wish that the three developers could find the time and the resources to port it to Firefox, Opera, Safari …

on Settings

Settings however used very infrequently are an important aspect of your product. When designing settings use clear titles and helper texts for not so straightforward settings. Make sure the settings are easy to find, make use of a search or group settings in a structured manner. A snapshot of the current status of the configuration helps users to choose the right setting.

Imran Parvez, Designing Settings

secure instant messaging

Which app could you not live without?

I love and rely on many of the apps I mentioned above. I’ve saved one to mention here, though: Threema. I love how easy it is to use and how secure it is for messaging. When traveling in places that aren’t as safe as others, it’s important to have this means of communication with my wife and organization. Because encryption is end-to-end and keys aren’t stored centrally, it really minimizes the risk of snooping and allows for open conversation. Add to that the self-destruct tagged onto the passcode failure and you’ve got a communication platform in which you can be confident. I’m constantly trying to convert iOS/Android/Windows Phone friends to Threema.

Brandon Jones’ Mac and iPhone setup

My swiss colleague Andreas is the only person I know in real life that uses Threema, alongside with his own swiss parents. I was also curious to use it, but since there’s no-one using it, there’s no point in spending money for it. And Telegram + Whatsapp will do (for the moment)…

Transloader, download a file on your Mac while working with your iPhone / iPad

Transloader running on a Mac

Ever come across a large zip or dmg file you wanted to download on your iPhone? Of course, you can’t do it. But with Transloader, you can. How? Transloader lets you download URLs from your iPhone, iPad or iPod touch directly to your Mac via iCloud.

Today, thanks to TwoDollarsTuesday, this amazing app by Matthias Gansrigler – founder & main developer of Eternal Storms Software – has been available with a stunning -67% discounted price.

With Transloader you can get the URLs to any kind of file you discover while reading an email, a feed or a post while you’re on the move with your iPhone (or iPad and iPod touch too) and it will sync them to your Mac for download. The iOS app is freely available, while the OS X “client” is the application you pay for.

The app is extremely useful – to me at least!!! – and Matthias Gansrigler is that cool kind of developer always willing to give an hand, offer support and – amazingly – even promo codes to his most loyal followers (don’t you believe me? check him out!).