Author: LCK (Page 2 of 13)

A physicist on the move...

Fixing Emacs tramp mode when using zsh

2 March 2016 / LCK / 8 Comments

Today I finally took some time to fix a long-standing problem: when trying to edit a file on a remote host using Emacs tramp mode, long time-outs occurred when typing the remote file name (after hitting C-x C-f). These time-outs were so long and occurred after each key press that tramp was effectively useless.

After some digging (e.g. excluding helm as the problem source) I found this entry in the Emacs Wiki which basically told my that using zsh (the Z shell) on the remote host could be the culprit. Indeed, after adding

[[ $TERM == "dumb" ]] && unsetopt zle && PS1='$ ' && return

at the top of my ~/.zshrc file solved the problem instantly. What this line does is simply replacing the shell prompt with a very simple one (a $ followed by a space) if the terminal is of the dumb type (which is the case for tramp).

Installing parted during Ubuntu installation

22 February 2016 / LCK / 0 Comments

When installing Ubuntu (I guess a regular Debian installation won’t be any different), I sometimes would like to manually create or change partitions (by jumping to another terminal, e.g. using Alt-F2) before doing the actual install. My preferred tool for that is parted, however, on regular Ubuntu installation images (at least the server variety), parted isn’t available from the console by default.

Today I noticed that (at least on today’s daily image of Ubuntu 16.04 Xenial), a udeb file for parted is available. This is how you install it:

udpkg -i /cdrom/pool/main/p/parted/parted-udeb_3.2-15_amd64.udeb

after which you can use parted to your heart’s content.

For more information on udebs see the Debian Installer Internals documentation.

Setting the console font when using an nVidia card

17 October 2015 / LCK / 0 Comments

Even though I do most of the work I do on my workstation in a graphical desktop environment, I sometimes want or need to switch to one of the virtual terminals (consoles), for example when trying to fix a connection problem or hanging desktop environment.

Whenever I had to do this I was always bothered by the fact that the font was so large (or, the other way around, the resolution so low). What made my annoyance worse was that I knew from my early Linux days So, instead of being annoyed I decided to fix this. Thanks to the help of mchid on unix.stackexchange.com I solved in a matter of minutes. The tricky part for me was to realise I am using an nVidia graphics card, which means things are just a little bit different than normally.

Just in case StackExchange ever goes down or this answer gets lost I will reproduce it below.

For newer Debian & Ubuntu distros using nvidia, I had to do the following: First, edit /etc/default/grub. Change the following line:

#GRUB_GFXMODE=640x480

to this:

GRUB_GFXMODE=1920x1200
GRUB_GFXPAYLOAD_LINUX=keep

replacing 1280×800 with the desired resolution.

Then:

echo "echo FRAMEBUFFER=y" | sudo tee /etc/initramfs-tools/conf.d/splash
sudo update-initramfs -u
sudo update-grub

To simply change the font size, you can do so using the following command:

sudo dpkg-reconfigure console-setup

Converting a PDF file to a PNG file

16 October 2015 / LCK / 0 Comments

Although ideally I try to create and use PDF files whenever I create something that is to be printed or even used on screen. It’s a universal, well defined open format. The added advantage is that is works well with vector graphics, something you really want for high quality material. However, sometimes external circumstances force you to deviate from your preferences. Yesterday I needed to import a PDF image into a LibreOffice Impress presentation. Unfortunately Impress can’t import PDF images. So I decided to convert my PDF image to a PNG file. My first idea was to use the convert utility:

convert file.pdf file.png

However, the default resolution was too low (and can be corrected using the -r option), but more importantly, I had some colour problems that I didn’t know how to correct.

I quickly looked around on the web and found this answer on superuser.com that pointed me to the pdftoppm tool. That worked brilliantly:

pdftoppm -r 1200 -png file.pdf > file.png

Configuring Org2blog

6 September 2015 / LCK / 0 Comments

Yesterday I installed Org2blog, which allows me to write my blog posts in Emacs org-mode and push them to my WordPress blog from within Emacs. So far I like it a lot! One less reason to leave Emacs :-), and hopefully also a reason to blog more often. Other good things about keeping your blog posts in Emacs are:

You can simply export them to e.g. PDF. In my current setup it’s a easy as adding the line
```
#+LATEX_CLASS: lckartcl
```
somewhere at the top of the file (before the actual text of the post starts) to tell org-mode that it should use my personal LaTeX export style, followed by C-c C-e l o and a nicely formatted PDF of my blog post pops up.
You keep all your blog posts in plain text format, so if you would decide to change to a different blogging platform, uploading the old posts should be fairly easy.

Org2blog’s GitHub page mentions C-c p as prefix key for Org2blog’s functions, but in my case this prefix is already used by Projectile, and looking in Org2blog’s Customize Group I noticed that C-c M-p is an alternative prefix, so I’m using that to get the following functionality:

`C-c M-p p`	publish buffer
`C-c M-p P`	post buffer as page and publish
`C-c M-p d`	post buffer as draft
`C-c M-p D`	post buffer as page draft
`C-c M-p t`	complete category

This is the Org2blog configuration in my .emacs file (note that I’m using John Wiegley’s use-package macro):

;;;;;;;;;;;;;;;;;;;;
;; Configure Org2blog, which allows me to write blog posts in org-mode
;; and then push them to my WordPress blog.
(use-package org2blog
  :config
  (require 'org2blog-autoloads)
  (setq org2blog/wp-blog-alist
        '(("blog.karssen.org"
           :url "https://blog.karssen.org/xmlrpc.php"
           :username "xxxxxx"
           :default-title "New blog post"
           :default-categories "Linux"
           :tags-as-categories nil)))
  )

Upgrading to Org-mode 8.3 via the package repository: fixing an error

5 September 2015 / LCK / 2 Comments

Today I tried to upgrade Emacs Org-mode to version 8.3. I used the regular package upgrade, but got the following error:

Invalid function: org-babel-header-args-safe-fn

Unfortunately, Irreal’s advice to byte-compile ob-R.el (twice) didn’t work out for me (by the way: thanks Planet Emacsen for aggregating so many useful posts!).

Browsing through some discussions on the emacs-orgmode mailing list it seemed that the error was due to org-mode being loaded while reinstalling the package. So I did the following:

I started emacs without loading my personal settings: emacs -Q

Next I ran the following code from my .emacs file in the scratch buffer (M-x eval-region) to set up the package manager:

(require 'package)
(package-initialize)
;; Add the original Emacs Lisp Package Archive
(add-to-list 'package-archives '("melpa" . "http://melpa.org/packages/") t)
;; Add the user-contributed repository
(add-to-list 'package-archives
             '("marmalade" . "http://marmalade-repo.org/packages/"))

And finally I used the package manager to remove and then install the latest org package.

Now all is fine again! 🙂

And by the way: this is my first blog post using Org2blog!

Experimenting with Google’s AdSense

2 September 2015 / LCK / 0 Comments

I don’t think this blog has any regular readers (especially since I’m not posting very regularly), but if they would exist they would have noticed two prominent changes in the last two days:

the WordPress theme for the site has changed, and
this blog now has several advertisements from Google’s AdSense programme.

Obviously, the two changes are tied together. From almost the first day of this blog’s existence I had been using the Carrington theme, and although I still like it a lot (including the fact that it has two columns on the left), its appearance on mobile devices was sub-par. To fix this I looked around for a theme with “responsive design” and the current one looks quite nice both on my desktop machines and on my phone.

Changing themes had been on my list for quite some time, but the reason that I took the time to actually do it was because of my idea to play around a bit with Google’s AdSense program. Apparently, Google likes it if a site looks well on all platforms. The main reason to add ads to this blog was to experiment a bit and simply to see if this is a viable way of recouping (some of) the costs associated with hosting this blog. I’ve got a decent number of monthly views (at least I think it’s decent 🙂 and it’s definitely more than I expected when I started out) so why not give it a try. Moreover, since this is my personal, low profile site, it can also give me an idea if it’s worth having advertisements on some of the community sites that I run.

So, all in all, I think the theme change is definitely a good one, and about the ads, we’ll see. Maybe it works out, maybe it doesn’t. All in all I hope they don’t interfere too much with normal reading of the site.

Using Magit to commit only some of the changes in a file

14 April 2015 / LCK / 0 Comments

As I discussed here, git allows you to commit only some of the changes you made to a given file. If you are working in Emacs you probably already know the wonders of Magit. In order to do the same partial committing of a file you can simply open magit-status and go to the file you’re interested in. This will highlight the changed parts of the text. With your cursor in the changed block you’d like to commit simply press s and that change will be staged. If this is all you want press c to commit and you’re done!

Source

DatABEL v0.9-6 has been published on CRAN

31 March 2015 / LCK / 0 Comments

This morning version 0.9-6 of the DatABEL R package was published on CRAN. This is only a minor update that consists of a few small changes and one bug fix. See the official announcement for more information.

DatABEL is an R package that allows users to access files with large matrices (of several gigabytes or more in size) in a fast and efficient manner. The package is mainly used for genome-wide association analyses using e.g. ProbABEL or OmicABEL.

GNU manifesto turns 30

30 March 2015 / LCK / 0 Comments

The New Yorker has a nice article about the GNU manifesto, which turned thirty earlier this month.
It nicely summarises what lead RMS to publish the manifesto and start the Free Software Foundation and also briefly explains the difference between Free Software and Open Source software.