I've managed to build and install (using checkinstall) an GNU Emacs 25.1 Debian package on 16.04, but on 16.10 for some unknown reason the compilation fails (at the make stage) giving the truncated output:

Loading language/czech...
Loading language/slovak...
Loading language/romanian...
Loading language/greek...
Loading language/hebrew...
Loading international/cp51932...
Loading international/eucjp-ms...
Loading language/japanese...
Loading language/korean...
Loading language/lao...
Loading language/tai-viet...
Loading language/thai...
Loading language/tibetan...
Loading language/vietnamese...
Loading language/misc-lang...
Loading language/utf-8-lang...
Loading language/georgian...
Loading language/khmer...
Loading language/burmese...
Loading language/cham...
Loading indent...
Loading emacs-lisp/cl-generic...
Loading frame...
Loading startup...
Loading term/tty-colors...
Loading font-core...
Loading facemenu...
Loading emacs-lisp/syntax...
Loading font-lock...
Loading jit-lock...
Loading mouse...
Loading scroll-bar...
Loading select...
Loading emacs-lisp/timer...
Loading isearch...
Loading rfn-eshadow...
Loading menu-bar...
Loading emacs-lisp/lisp...
Loading textmodes/page...
Loading register...
Loading textmodes/paragraphs...
Loading progmodes/prog-mode...
Loading emacs-lisp/lisp-mode...
Loading progmodes/elisp-mode...
Loading textmodes/text-mode...
Loading textmodes/fill...
Loading newcomment...
Loading replace...
Loading emacs-lisp/tabulated-list...
Loading buff-menu...
Loading fringe...
Loading emacs-lisp/regexp-opt...
Loading image...
Loading international/fontset...
Loading dnd...
Loading tool-bar...
Loading dynamic-setting...
Loading x-dnd...
Loading term/common-win...
Loading term/x-win...
Loading mwheel...
Loading emacs-lisp/float-sup...
Loading vc/vc-hooks...
Loading vc/ediff-hook...
Loading uniquify...
Loading electric...
Loading emacs-lisp/eldoc...
Loading cus-start...
Loading tooltip...
Loading /home/fusion809/Programs/emacs-25.1/lisp/leim/leim-list.el (source)...
Finding pointers to doc strings...
Finding pointers to doc strings...done
Dumping under the name emacs
Makefile:736: recipe for target 'bootstrap-emacs' failed
make[1]: *** [bootstrap-emacs] Segmentation fault (core dumped)
make[1]: Leaving directory '/home/fusion809/Programs/emacs-25.1/src'
Makefile:398: recipe for target 'src' failed
make: *** [src] Error 2

To be clear I ran:

./autogen.sh && ./configure --prefix=/usr --with-x-toolkit=gtk2 && make

and it was at the make stage that the build failed. I did run sudo apt-get build-dep -y emacs24 before running these commands.

EDIT: I can confirm that this segmentation fault occurs even when the --with-x-toolkit=gtk2 option is substituted with --with-x-toolkit=gtk3.

I ran sudo apt-get build-dep emacs24 and it returned the error:

Reading package lists... Done
E: Unable to find a source package for emacs24

Now I know the usual advice in this situation, that is, uncomment deb-src lines in the .list files in your /etc/apt/sources.list.d folder (per https://unix.stackexchange.com/questions/158395/apt-get-build-dep-is-unable-to-find-a-source-package). I've tried this though! Every single file in my /etc/apt/sources.list.d folder has any deb-src lines in it uncommented. I even ran sudo apt-get update after uncommenting these lines! So please help me. Here are the contents of my /etc/apt/sources.list.d folder, if you need the contents of any of these files, just say and I'll be happy to provide them.

$ ls /etc/apt/sources.list.d
alexlarsson-ubuntu-flatpak-xenial.list
alexlarsson-ubuntu-flatpak-xenial.list.save
cpick-ubuntu-hub-xenial.list
cpick-ubuntu-hub-xenial.list.save
damien-moore-ubuntu-codeblocks-stable-xenial.list
damien-moore-ubuntu-codeblocks-stable-xenial.list.save
danielrichter2007-ubuntu-grub-customizer-xenial.list
danielrichter2007-ubuntu-grub-customizer-xenial.list.save
docker.list
docker.list.save
dolik-rce-ubuntu-upp-xenial.list
dolik-rce-ubuntu-upp-xenial.list.save
dotnetdev.list
dotnetdev.list.save
gnome3-team-ubuntu-gnome3-staging-xenial.list
gnome3-team-ubuntu-gnome3-staging-xenial.list.save
gnome3-team-ubuntu-gnome3-xenial.list
gnome3-team-ubuntu-gnome3-xenial.list.save
google-chrome.list
google-chrome.list.save
google-earth.list
google-earth.list.save
icons.list
icons.list.save
jonathonf-ubuntu-golang-xenial.list
jonathonf-ubuntu-golang-xenial.list.save
kubuntu-ppa-ubuntu-backports-xenial.list
kubuntu-ppa-ubuntu-backports-xenial.list.save
mmk2410-ubuntu-eclipse-ide-java-xenial.list
mmk2410-ubuntu-eclipse-ide-java-xenial.list.save
mono-jenkins.list
mono-jenkins.list.save
mono-xamarin.list
mono-xamarin.list.save
nodesource.list
nodesource.list.save
noobslab-ubuntu-macbuntu-xenial.list
noobslab-ubuntu-macbuntu-xenial.list.save
notepadqq-team-ubuntu-notepadqq-xenial.list
notepadqq-team-ubuntu-notepadqq-xenial.list.save
runescape.list
runescape.list.save
saiarcot895-ubuntu-myppa-xenial.list
saiarcot895-ubuntu-myppa-xenial.list.save
spotify.list
spotify.list.save
trinity.list
trinity.list.save
ubuntu-elisp-ubuntu-ppa-xenial.list
ubuntu-elisp-ubuntu-ppa-xenial.list.save
unity8-desktop-session-team-ubuntu-unity8-preview-lxc-xenial.list
wine-ubuntu-wine-builds-xenial.list
wine-ubuntu-wine-builds-xenial.list.save

If relevant, and you can't tell by the previous bits of information I provided, I am operating on Ubuntu 16.04.1.

I have several Virtual machines (VMs) that run through VirtualBox that I have created desktop configuration files for and set custom icons (usually in .svg format, although to see whether this issue is localized just to SVG icons I have tried using .png icons, with no improvement in visibility) for. In other desktop environments such as Cinnamon, GNOME 3, LXDE, MATE, Unity and Xfce these custom icons are rendered perfectly fine, without issue, but for whatever reason in KDE (i.e., Kubuntu, installed via running sudo apt-get install kubuntu-desktop from terminator) these icons simply do not appear. The desktop configuration files do appear in the KDE application menu, but next to their names, where I would normally see their icon there's absolutely nothing shown. See for example, the screenshot below showing how they appear in the KDE application menu.

I also know that when I drag these VM machines from the KDE menu to the plasma panel the application launchers that appears in the panel also has no icon shown. This problem isn't limited to VM machines either, other programs like RuneScape Unix Client (RSU), Avogadro and GNU Octave also have missing icons.

I would like to optimize a SVG using software on Ubuntu (and by optimize I mean to reduce the file size without loosing any visible parts of the graphic) and I do mean software I know there are some websites that can do this but I don't trust my internet connection always being good enough for this to work for me. I would also like to keep the file format SVG, I know that SVGZ is usually substantially smaller than its uncompressed counterpart but I am uploading these SVGs to a local MediaWiki installation and it cannot thumbnail SVGZ files to my knowledge (if I'm wrong please do correct me).

I would like to set Thunar as my default file manager in 15.04. Now, I realize that this question is very similar to How to set Thunar as a default file manager?, but I have tried Kevin's answer, why I even tried rebooting after I completed his suggestion but still Nautilus is used as my default File Manager. I even tried the shell script, Midnight Commander and Manual solutions recommended on the Community Help Wiki. Not one changed Thunar to my default file manager.

I was curious as to whether exo could change my default file manager at all, say to dolphin (as I also saw this question and its answer) but that also failed. Something tells me that this issue affects not just me but other users too, specifically 15.04 users, as Ubuntuuser reported in the comments that he could not set dolphin as his default file manager via exo either.

If you would like to know how I am checking whether these file managers are set to default, well I open folders on my desktop by double-clicking them to see whether they're opened in these alternative file managers or not and as a second test I also try to save files in Chrome to see whether the file manager window that pops up is the one I want.

If relevant I am running Unity as my Desktop Environment.

I installed POV-Ray by running sudo apt-get install povray but now whenever I run:

povray Jmol.pov.ini

I get the error:

povray: cannot open the user configuration file /home/fusion809/.povray/3.7/povray.conf: No such file or directory

Problem with option setting
povray /home/fusion809/Chem Structures/Crystal structures/Jmol.pov.ini
Failed to parse command-line option

where Jmol.pov.ini is the ini file, that is in the same directory as its corresponding pov file, and both were produced by Jmol. I feared that I may have foolishly removed my .povray directory (as the directory doesn't exist at the location specified in this error message) so I reinstalled povray by running:

sudo apt-get install povray --reinstall 

But unfortunately the .povray directory still doesn't exist and I still get the same error.

On Chemistry Stack Exchange I asked a question regarding Open Babel & Python being used together.

The problem is that the answer I was provided (by Geoff Hutchinson) requires Python to be able to import the module Pybel.

I have installed Open Babel on this PC via two ways, APT and source. I then deleted my APT installation after I realized pybel wasn't available for Python use and I decided to install from source with Python bindings.

To do so I followed this guide with the final command being customized to (running from ~/build)

cmake ../openbabel-2.3.2 -DBUILD_GUI=ON -DPYTHON_BINDINGS=ON

which gave the output:

-- Using included inchi library.
-- Found wxWidgets: TRUE  
-- Cairo found. PNG output will be supported.
-- Attempting to build the GUI
--    wxWidgets found => GUI will be built
CMake Warning (dev) at test/CMakeLists.txt:171 (include):
  Syntax Warning in cmake code at

    /home/fusion809/Downloads/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:54:14

  Argument not separated from preceding token by whitespace.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at test/CMakeLists.txt:171 (include):
  Syntax Warning in cmake code at

    /home/fusion809/Downloads/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:54:31

  Argument not separated from preceding token by whitespace.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at test/CMakeLists.txt:171 (include):
  Syntax Warning in cmake code at

    /home/fusion809/Downloads/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:57:25

  Argument not separated from preceding token by whitespace.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at test/CMakeLists.txt:171 (include):
  Syntax Warning in cmake code at

    /home/fusion809/Downloads/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:57:39

  Argument not separated from preceding token by whitespace.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Python bindings will be compiled
-- Could NOT find Ruby (missing:  RUBY_INCLUDE_DIR RUBY_LIBRARY RUBY_CONFIG_INCLUDE_DIR) (found version "2.1.0")
-- Ruby library files NOT found. Ruby bindings will NOT be compiled.
-- Configuring done
-- Generating done
-- Build files have been written to: /home/fusion809/build

I should mention, however, that the first time I compiled Open Babel I forgot to add the -DBUILD_GUI & -DPYTHON_BINDINGS commands to the cmake line, so I had to run this new cmake command after I had initially compiled the software. Does this make any difference? Should I remove Open Babel and re-compile? If so do I have to delete some files in my /usr/ directory to (if so please mention them as I don't know which ones)? If relevant I am on 32 bit 15.04.

EDIT

I deleted my build directory's contents & started again and after the cmake command I ran:

make
sudo make install
export PYTHONPATH=/usr/local/lib:$PYTHONPATH

At the end of the output I received were these two lines:

-- Up-to-date: /usr/local/lib/openbabel.py
-- Up-to-date: /usr/local/lib/pybel.py

In a Python terminal I ran import openbabel and import pybel and it gave the output: ImportError: No module named ... where ... is openbabel or pybel, depending on which of the commands were executed, so I suspect it's a problem on my Python installation's end.

I'd like to be able to crop SVG chemical structures, completely (see this question), that were created using MarvinSketch and I think I might have thought of a solution; I use MarvinSketch to create a large PNG file, then crop that using GIMP, and then convert the PNG to SVG. Hence I'd like to know if anybody knows a free software I can install (I don't like using online converters as I'm always suspicious of malware) on Ubuntu for high quality PNG->SVG conversion.

I ask because Ubuntu Tweak's Janitor is frozen due to the sheer number of packages in the cache that accumulated during the upgrade from 12.10 to 13.04.

After I upgraded to 13.04 my desktop background has been a black screen, i.e.:

EDITS: Ubuntu tweak doesn't seem to be able to change the window theme either (although all other themes like icon themes are all easily modifiable). Tweak tool can change the window theme, however.

I have tried the following:

• Changing desktop backgrounds (including back to default)
• Rebooting
• Running the commands in terminal: (Which were obtained from the answer to the question, Unity does not start in Ubuntu 13.04)

dconf reset -f /org/compiz/ && unity --reset-icons &disown

and then rebooting (which just changed the colour and size of the unity launcher)

• What is laid out here http://falkvinge.net/2013/02/15/how-to-install-nvidia-drivers-in-ubuntu-12-10-quantal/.
• dconf reset -f /org/compiz/ && gnome-session-quit in terminal
• unity --reset (which gave the output: ERROR: the reset option is now deprecated)
• unity --replace
• What's outlined here: https://askubuntu.com/a/286774/93125

An example of what I'm talking about is this animation from Wikipedia. I am running 32 bit 12.10 if it is relevant. Please describe step-by-step, with pictures (screenshots with the appropriate areas (that are mentioned in the text) highlighted) how I am to create these gif files with the software you name.

What Free Ubuntu-Compatible Software Exists for the 3D Visualisation of Biologic Proteins and Peptides? I asked this question https://chemistry.stackexchange.com/questions/4543/what-free-linux-compatible-software-exists-for-the-3d-virtualisation-of-biologic? but it got closed because it was software recommendation which is off-topic for chemistry stackexchange but I thought it wouldn't be off-topic for here. I am running 32 bit 12.10 if it is relevant.

How do I change the bucket fill colour in Gimp Image Editor?

Now by sorted tables I should clarify. I'd like LibreOffice calc to create tables with the same functionalities as those formed in Microsoft Excel 2007/2010 when the table data is selected and ctrl+T is pressed. When I sort a column I want all the columns to change accordingly so that each row is lined up properly. I am running LibreOffice 3.6.4 on 12.10 if these details are necessary.

I know that LibreOffice Writer can facilitate subscripts and superscripts in ordinary, non-formula, text—when I copy and paste such things from Microsoft Office Word 2007 documents LibreOffice Writer manages to accommodate them. My LibreOffice Writer version is 3.6.4.

I haven't managed to find any better place to ask this question, if there is please direct me to it. I am running 12.10 if it is relevant.

Additional details are:

OS = 12.10

Present Default Torrent Application = qBittorrent

Preferred Default Torrent Application = Vuze

My main area in of which I'm looking for advise is magnet links. Plus the program in question isn't 'installed' per say I have downloaded the tarball file for Vuze and I run the executable file from there to run it.

Whenever I open up the page http://www.runescape.com/game.ws? in google chrome I get the notice, "IcedTea was blocked because it is out of date" and gives me the two options of updating it or running this time.

I've gone to the link attached to the option of updating it and its a wikipedia page http://icedtea.classpath.org/wiki/Main_Page that wasn't helpful for me because I didn't know what to download and install.

Whenever I click, 'Run this time' it works momentarily but it is prone to have the runescape interface in the browser disappear and be replaced with a black screen.

Basically as is the title how do you install Myunity on 12.10? I've tried adding the repository ppa:myunity/ppa and performing:

sudo add-apt-repository ppa:myunity/ppa
sudo apt-get update
sudo apt-get install myunity

At which point I received the error:

W: Failed to fetch http://ppa.launchpad.net/myunity/ppa/ubuntu/dists/quantal/main/binary-i386/Packages  404  Not Found

E: Some index files failed to download. They have been ignored, or old ones used instead.

Basically as per question. I have the .tar.gz file but I can't seem to install it. I did the whole, ./configure, make and make install but it didn't work.

Yet again I am to turn to this wonderful resource available to me and ask, how do I install the latest version of GNU Octave (not Octave 3.2.4 -- the one available in the software centre)?