The demise of gksudo from Ubuntu-based distributions and what to do about it

I gather that there were good security-related reasons for discontinuing gksudo. But it's quite inconvenient not having it, for example when you are adding new items to the Linux Mint main menu (using menulibre, for example).

Here's what I do:

• install ssh-askpass
  
  
• add this line
  

  SUDO_ASKPASS=/usr/bin/ssh-askpass
  

  to the file

  /etc/environment

• Then, in menu or batch commands that you want to pop-up a graphical p/w prompt, say
  

  sudo -A <command>

Automounting google-drive-ocamlfuse: getting Google Drive to appear as a Linux folder

This is well documented elsewhere, but just for clarity, here are my settings, that work. I.e., the Google drive appears automatically mounted after a fresh boot.

1. Install google-drive-ocamlfuse

2. Line in /etc/fstab (all one line):

gdfuse#default  /home/dom/GoogleDriveUofA    fuse    uid=1000,gid=1000,allow_other,user,_netdev     0       0

3. Contents of executable /usr/bin/gdfuse

#!/bin/bash
su dom -l -c "google-drive-ocamlfuse -label $1 $*"
exit 0

Linux Mint 19.1 Cinnamon and display flickering

When I upgraded to Linux Mint 19.1 with Cinnamon, I encountered a problem that my screen flickered immediately after logging in.  Others encountered the same problem (here).
I found that the solution proposed there, i.e., to delete the line

CLUTTER_PAINT=disable-clipped-redraws:disable-culling

from the file

/etc/environment

worked for me.  Logging out and back in after that change gave me a stable display.

Fetching multiple files from an internet site as a batch job

Sometimes one encounters a website that displays a book or manuscript page-by-page as individual jpeg files.  But what you need for your research is to have a single PDF of the item, so that you can move about it easily, and consult it offline.

There are several quick ways of getting these images as a batch job: here's one.   

• First you have to identify the URL of one of the images.  I use Firefox, so I 
  • first bring up a page that displays the first folio of the MS. 
  • Then I press ctrl+I to get the "page info" (or Firefox menu Tools/Page Info).  
  • Then I select "Media" on the top line of the Info window.  
  • Then scroll down to the graphics file of the whole page, right click and ctrl+c to copy the URL.
    
    You now have a URL that looks like this:
    
    http://awebsite.net/uploads/manuscripts/miscellaneous/sometext/001.jpg

There may be a more direct way of getting this URL, but this is good enough for me.

The next bit is the nice bit.  Drop to the command line and use the utility "curl".  Here's the syntax ($ is my command prompt):

$ curl -O http://awebsite.net/uploads/manuscripts/miscellaneous/sometext/[001-268].jpg

• Hit "enter" and several hundred jpeg files will be transferred to your directory.  It takes a couple of minutes, depending on your bandwidth.
  The bit in square brackets, "[001-268]" is curl's syntax for "please fetch 001.jpg, 002.jpg, ... 267.jpg, and 268.jpg".  Curl is one of the few tools with this simple ability to fetch lots of different files with a single simple command.

To convert them to a single PDF, I use ImageMagick:

$ convert *.jpg Hayanaratna.pdf

and wait for ten seconds.

(I was taught about curl by Patrick McAllister - thanks Patrick!)

A quite different approach is to use wget to fetch a whole website in a single gulp.   That's what I use for GRETIL, for example, so that I have the whole archive on my hard drive.

Tweaking the Thinkpad's TrackPoint settings in Linux Mint 19

With the update to Linux Mint 19 Cinnamon, the sliders controlling the trackpoint's accelleration and speed on my Thinkpad T560 and T500 don't work any more.  I expect it will get fixed soon.  Meanwhile, as root I  can manually edit the parameters in the filesin the directory

• /sys/devices/platform/i8042/serio1/serio2

The above directory is found by

• find /sys/devices/platform/i8042 -name name | xargs grep -Fl TrackPoint | sed 's/\/input\/input[0-9]*\/name$//'

Settings are reset at reboot.  :-(

I like sensitivity 125 and speed 80 on the T560; 190 and 90, inertia 10, on the T500.

Update

I found this solution (X1 parameters) that automates everything and survives reboot :-)

Another update, March 2020

Lalufu at github said,

You can also use xinput to modify the libinput values directly:
Run xinput to show the pointers the system knows about. If you have a ThinkPad you should see something along the lines of TPPS/2 IBM TrackPoint or similar.

xinput --set-prop "TPPS/2 IBM TrackPoint" "libinput Accel Speed" -0.5

will modify the pointer speed. Play around with the value to see what you like. If you want this to survive a reboot you can stick this in .bash_profile.

Improving PDFs

I sometimes  do some processing on PDFs if I think they are important, or I want to read them more conveniently.  I was trying to explain my techniques to my students, recently, and I realized that I use a mixture of tools that are not at all obvious or easy to explain to someone not familiar with Unix.
So I'm going to write down here what I do, so that at least the information is available in one place.  I assume a general knowledge of Linux and an ability to work with command-line commands.

If I receive a PDF that is a scanned book, with 1 PDF page = one book opening, I want to chop it up so that 1 PDF page = 1 book page.

• make a working directory
• use pdftk to unpack the PDF into one file per page:
  

  > pdftk foobar.pdf burst

• I now have a directory full of one-page PDFs.  Nice.
• convert them into jpegs using pdf2jpegs, a shell script that I wrote that contains this text:
  

  #!/bin/bash
  # convert a directory full of pdfs into jpegs
  for i in *.pdf; do pdftoppm -jpeg -r 400 "$i" >"$i.jpg"; done

• I now have a directory full of jpegs, one jpeg per page.
• Start the utility scan-tailor and use it to
  
  • separate left and right pages into separate files
  • straighten the pages
  • select the text area of each page
  • create a margin around the text
  • finally, write out the resulting new pages
   
• I now have a directory (../out) full of TIFF files, one page per file, smart.
•  Combine the TIFFs into a single PDF using my shell script tiffs2pdf:
  

  #!/bin/bash
  # Create a PDF file from all the .tiff files in the current directory.
  # The argument provides the name of the output file (with .pdf appended).
  echo "Created a PDF from a directory full of .tif files"
  echo "Single argument - the filename of the output PDF (no .pdf extension)"
  tiffcp *.tif "/tmp/${1}.tiff"
  tiff2pdf "/tmp/${1}.tiff" > "${1}.pdf"
  echo "Created ${1}.pdf"
  rm "/tmp/${1}.tiff"
  echo "Removed temporary file /tmp/${1}.tiff"
  
  # thanks to http://ubuntuforums.org/showthread.php?t=155628

   
• I now have a nice PDF that has one smart page per PDF page. 
• If I want it OCRed, then I usually use Adobe Acrobat, a commercial program. But if I'm uploading to Archive.org, that isn't necessary because Archive.org does the OCR work using Abbyy.

That's all, folks!

Helpful notes on bulk downloading from Archive.org

• https://gareth.halfacree.co.uk/2013/04/bulk-downloading-collections-from-archive-org
• https://pypi.python.org/pypi/internetarchive

Much easier to work with a compiled ia rather than the python version (which I couldn't get to work anyhow).

Del latitude xinput settings

See https://askubuntu.com/questions/688270/mouse-speed-too-fast

Put the following commands in a file (foobar.sh), make the file executable (chmod +x foobar.sh), and then run it.

#!/bin/sh
xinput --set-prop "AlpsPS/2 ALPS DualPoint Stick" "Device Accel Constant Deceleration" 8
xinput --set-prop "AlpsPS/2 ALPS DualPoint Stick" "Device Accel Velocity Scaling" .8
xinput --set-prop "AlpsPS/2 ALPS DualPoint Stick" "Device Accel Adaptive Deceleration" 8


You can run this command on startup from the Startup Applications menu.

IBUS bug fix ... again (sigh!)

Further to https://cikitsa.blogspot.ca/2012/01/ibus-bug-fix.html, I found the same bug cropping up in Linux Mint 18.1, with IBUS 1.15.11.

Some applications don't like IBUS + m17n, and certain input mim files. For example, LibreOffice and JabRef.  Trying to type "ācārya" will give the result is "ācāry a". And in other strings, some letters are inverted: "is" becomes "si" and so forth.

Here's the fix.

Create a file called, say ibus-setting.sh with the following one-line content:

export IBUS_ENABLE_SYNC_MODE=0

Copy the file ibus-setting.sh to the directory /etc/profile.d/, like this:

sudo cp ibus-setting.sh /etc/profile.d

Make the file executable, like this:

sudo chmod +x /etc/profile.d/ibus-setting.sh

Logout and login again.

Phew!

This fixes the behaviour of IBUS + m17n with most applications, including LibreOffice and Java applications like JabRef.  However, some applications compiled with QT5 still have problems.  So, for example, you have to use the version of TeXStudio that is compiled with QT4, not QT5. [Update September 2018: QT5 now works fine with Ibus, so one can use the QT5 version of TeXstudio with no problem.]

GNU Freefont fonts and XeLaTeX

The problem

There's been a long-standing issue about using the Gnu Freefont fonts with XeLaTeX.  The fonts are "Free Serif", "Free Sans" "Free Mono", and each has normal, italic, bold and bold-italic versions.  

These fonts are maintained by Stevan White, who has done a lot of support and maintenance work on them.  

These fonts are of special interest to people who type Indian languages because they include nice, and rather complete Devanāgarī character sets in addition to glyphs for

• Bengali
• Gujarati
• Gurmukhi
• Oriya
• Sinhala
• Tamil
  and
• Malayalam

The Gnu Freefonts are excellent for an exceptionally wide range of scripts and languages, as well as symbols.  See the coverage chart.

At the time of writing this blog, December 2014, the release version of the fonts is 4-beta, dated May 2012.  This is the release that's distributed with TeXLive 2014, and is generally available with other programs that include or require the FreeFonts.

But the 2012 release of the FreeFonts causes problems with the current versions of XeTeX.  Basically, the Devanagari conjunct consonants in the 2012 fonts are incompatible with the current XeTeX compositing engine. (For the technical: Up to TL 2012 XeTeX used ICU; since TL 2013 it's used HarfBuzz.)

In the last couple of years, Stevan has done a great deal of work on the Devanagari parts of the FreeFonts, and he has solved these problems.  But his improvements and developments are only available in the Subversion repository.   For technically-able users, it's not hard to download and compile this pre-release version of the fonts.  But then to make sure that XeTeX calls the right version of the FreeFonts, it's also necessary to weed out the 2012 version of the fonts that's distributed with TeX Live 2014.  And that's a bit hard.  In short, things get fiddly.

Now, Norbert Preining has created a special TeX Live repository for the Subversion version of the FreeFonts.  TeX Live 2014 users can now just invoke that repo and sit back and enjoy the correct Devanagari typesetting.

New warning June 2017: 
the procedure below is no longer supported.  Don't do it.

WARNING
Be warned that the version distributed here is a development version, not meant for production. Expect severe breakage. You need to know what you are doing!
END WARNING

Here follow Norbert's instructions (as of Dec 2014).  Remember to use sudo if you have TeX Live installed system-wide.

The solution. A new TeX Live repository for the pre-release Gnu FreeFonts

Norbert says (Dec 2014):

Here we go: Please do:

tlmgr repository add http://www.tug.org/~preining/tlptexlive/ tlptexlive
tlmgr pinning add tlptexlive gnu-freefont
tlmgr install --reinstall gnu-freefont

You should see something like:  

[~] tlmgr install --reinstall gnu-freefont
...
[1/1, ??:??/??:??] reinstall: gnu-freefont @tlptexlive [12311k]
...

Note the

@tlptexlive

After that you can do  

tlmgr info gnu-freefont

and should see: 

Package installed:   Yes
revision:    3007
sizes:       src: 27157k, doc: 961k, run: 19769k
relocatable: No
collection:  collection-fontsextra

Note the

revision: 3007

which corresponds to the freefont subversion revision!!!

From now on, after the pinning action, updates for gnu-freefont will

always be pulled from tlptexlive (see man page of tlmgr).
 

Reverting the change:

In case you ever want to return to the versions as distributed in TeX Live, please do

tlmgr pinning remove tlptexlive gnu-freefont
tlmgr install --reinstall gun-freefont

Thank you, Norbert!

Linux Mint 17, Cinnamon, Firefox 31 = freeze

I've been very happy with Linux Mint 17, and the Cinnamon GUI.
Except for the occasional system freezes.  This happened usually when I was swapping between windows (alt+tab), and required a re-login.

I've spent some time looking around the web and trying to diagnose the problem.  I've found one change that seems to have cleared up the problem, and I am not aware that anyone else has mentioned it yet.  I've uninstalled Firefox (31), and replaced it with Google Chrome.  I haven't had a freeze since doing that.  Fingers crossed.

Corrupted font spacing in terminal

I had this problem, that was solved by purging pango-graphite:

sudo apt-get purge pango-graphite

From Gnome to Cinnamon

Gnome 2 and 3

Ubuntu with Gnome 2

Ubuntu with Unity

After moving to Ubuntu GNU/Linux for all my work, in 2009, I used the default interface, Gnome 2, for a while.  Later, with version 3, Gnome moved to a completely new concept, but Ubuntu forked the development and moved to Unity, so I did that too.  

Gnome 3

Gnome 2 and Unity both had their virtues and their flaws.  The six-monthly upgrade cycle ("cadence") was never as smooth as it should be, so there have often been niggles that lasted a few weeks or months.  I didn't like Unity's two different search boxes.

Ubuntu with Gnome 3

I started using the Gnome Shell, ver. 3, on Linux (Ubuntu) after seeing my friends and colleagues using it at the TeX conference in Trivandrum in 2011.  I really liked Gnome 3, but with the update from 3.6 to 3.8 and 3.10, they did some major, major things wrong, and I've finally dumped it, in favour of Cinnamon.

The biggest boo-boo in the development of Gnome from version 3.8, was fooling with the default file-manager, Nautilus.  Many people have complained about the stripping out of function, like split-screen, and that was bad enough.  So was the nonsense about shifting the menus to the panel bar (or not!).  But what hasn't got mentioned so much (at all?) is that the new Nautilus changed all the keyboard shortcuts and rearranged the shortcuts relating to the menu system.  So Alt-F didn't bring up a "File" menu any more, for  example.  Right mouse-click+R didn't begin renaming a file.  If one uses computers all day, then one's fingers get trained, and no interface designer should mess with that stuff without expecting backlash.  With Nautilus 3.8, it was like being a beginning typist again, looking at my fingers, chicken-pecking for keys.

I liked the general design model of Gnome 3, with the corner switch to the meta level for choosing programs, desktops, and so on.  Searching for lesser-used programs with a few keystrokes rather than poking hopelessly through nested menus.  Much better.  A genuine and valuable contribution to the vision of how a computer should work.

Thanks to Webupd8, I was able to work around the Nautilus problem by uninstalling it and using Nemo instead.

But things just kept going wrong.  The shell crashed too often.  On two of my machines it stopped coming up at login, and had to be started manually.  Only after a couple of weeks did I track this down to a bad file in ~/.config/gnome-session (and I'm still not 100% sure).  Frequent crashes of the gnome-control-panel and other utilities.  More and more extraordinary tweaking to make it comfortable and useable.  Finally, I've had enough.

 

Cinnamon

Ubuntu with Cinnamon

I'm in my first few days of using Cinnamon, and so far things are okay.  I'm running Cinnamon on top of Ubuntu.  It's like stepping back in time, a bit, all those menus.  But one doesn't have to use them, and with a bit of tweaking one can set things up so that actual shell behaviour is very similar to Gnome 3.6.  Nemo is there - what a relief.  Alacarte actually works, but I've dumped it in favour of Menulibre in any case.  Configuration and tweaking is much nicer.  Many useful add-ons, and although I liked the http://extensions.gnome.org system, Cinnamon handles the add-on business in a much more integrated way.  Ibus+m17n work as expected again.  In general, it's an update from Gnome 2 in the direction of Gnome 3 but not the whole way.  And it seems more stable, which is critical to getting work done.

Checklist of things to do on reinstalling Ubuntu

I'm finally moving to 64 bit Linux (since all my machines are fine with that).  My disks have my /home and root files in different partitions, so I can erase and reinstall Linux itself without touching any of "my" files.  This works flawlessly, and the new installation comes up with all my old desktop settings etc.  Since the Ubuntu Software Center's "sync" function still doesn't work properly, here are some installations and customizations that I like:

Xapian niceness

In older Linuxes, if xapian indexing is sucking up all your CPU cycles, here's a fix:

• http://ubuntuforums.org/showthread.php?p=9304431#post9304431

I believe this is long ago fixed in Ubuntu releases and doesn't need to be done manually.

A gold star for Gnome 3

When Canonical decided that Ubuntu would have a new user-interface, "Unity," to replace Gnome 2, there was a lot resistance and discontent in the Ubuntu user community.  Gnome 2 was a drop-down (or pop-up) menu system, harking back in a general way to the familiar Windows interface.

People who didn't like Unity could easily just go on using Gnome 2, at least for the foreseeable future (and switch to MATE after Gnome 2).

But the other alternative was to use Gnome 3, the official successor to Gnome 2.  Gnome 3 and Unity have quite a lot in common.  In fact, and it's clear that the Unity user interface is - broadly speaking - based on the same thinking as Gnome 3 about where user interfaces might be going.

As is documented in this blog, I was willing to give Unity a shot, and I even quite liked it.  But I had a lot of technical difficulties with Unity, so I decided to try Gnome 3.

Now I've been using Gnome 3 for nearly six months, and I'm very much at home with it.  And I'd like to put in a good word.  Recently, I had to work briefly with the old  Gnome 2 menus, and I couldn't believe how slow and fiddly the old interface now felt, after being thoroughly used to Gnome 3.

So, from me, at least, a gold star for Gnome 3.

T500+ubuntu 11.10 = slow wifi network access

News, November 2012: 

The problem described below went away with the upgrade to Ubuntu 12.10 (Linux kernel 3.5).  Thank goodness, and high time.
 
--

There's a bug between the Thinkpad T500 and wireless n transmission.

Bug discussion here, fix here, thanks to Damon:

sudo rmmod iwlagn
sudo echo "options iwlagn 11n_disable=1" > /etc/modprobe.d/disable11n.conf
sudo modprobe iwlagn

ibus bug fix

Typing Sanskrit in Ubuntu Linux is normally very convenient, using the built-in ibus and m17n systems.  You can write देवनागरी or romanisation (devanāgarī) with just a switch of the keyboard input method. (Thansiang's input method for romanisation input is effective and convenient, but has to be added manually because it isn't included in the main m17n distribution.)

However, with the update to Ubuntu 11.10 in October 2011, a bug was introduced that spoiled typing for several Asian languages, for users of the standard Ubuntu Unity and Gnome windows managers.  The symptom was that as you typed a space, the letters around the cursor jumped into the wrong order. 

The November solution by fujiwarat fixed things.  But it hasn't yet made its way into the standard Ubuntu updates.  At the time of writing, you have to update your ibus installation to version 1.4.0 manually. One way to do it is here, kindly provided by Alex Lee.

March 2012 Update (gnome-shell)

Brandon Schaefer has fixed this ibus/unity bug (thanks!), but the fix will only be released in Ubuntu 12.04 Precise Panglin.  Schaefer asks Oneiric users to wait a couple of months, since,

The changes would be to large and would require changes 

in both unityand nux. 

This is good for the future, but isn't great news for anyone who needs to type in an Asian language during the next two months.

And since ibus and the patch have moved along since the posting above, on 14 Jan, Alex Lee's instructions don't work any more.

The deb files that I made for myself in January, following Alex Lee's instructions are available here for a few months:

•  ibus1.4.0 for Oneiric 

Fetch the six files, put them in a directory, and run the following two commands in a terminal, in the directory containing the deb files:

• sudo apt-get remove ibus 
• sudo dpkg -i *.deb
• sudo apt-get install m17n

Log out and in for good measure, though it may not always be necessary.

Hope it works for you.  No guarantees, and no further help available from me, I'm afraid.   There has been a post suggesting that this does not work under unity (see here).  More testing required.  But it works fine for me under gnome-shell, and probably the other non-unity interfaces.

April 2012 update

All the above problems are solved in the 12.04 Precise Pangolin release of Ubuntu.  Just go with the defaults.

Furthermore, Pangolin's release now includes the input of Sanskrit roman transliteration as standard, using the IAST standard.  It's very nice.

Oneiric Ocelot upgrade woes

My main desktop machine got in a terrible mess during the Oneiric update.  Could have been my fault - I started the update and then left the machine for two days.  When I got back to it, it was frozen, and on hard reboot it wouldn't boot.  Finally, I got it back by booting from a USB stick and then using chroot to get a pseudo-login as root on the hard disk.

• http://karuppuswamy.com/wordpress/2010/06/02/how-to-chroot-to-ubuntu-using-live-cd-to-fix-grub-rescue-prompt/

Having a network connection, that enabled me to clean up the system with dpkg and apt-get, so I fetched all the latest versions of everything and updated and upgraded tidily.  But still couldn't get a boot because of an obscure network problem with connecting to the bus.  Finally solved by these (weirdly written) instructions:

• http://journalxtra.com/2011/10/upgrade-oneiric-ocelot/

Now up and running, amazingly.


--

and another thing...

The compiz grid feature developed a fault about putting a window on the top-right of the screen.  Solution is here: https://launchpad.net/~lbrulet-8/+archive/ppa

Ubuntu Evince menu fonts turn to garbage

Grr, recurrence of the old, old problem that the Evince menus turn to little squares like this:

Solution:

• http://ubuntuforums.org/showpost.php?p=8216711&postcount=4, 
  that says:

sudo mv /etc/apparmor.d/usr.bin.evince ~/
sudo /etc/init.d/apparmor restart