Tag Archive for update

Sorting out MySQL on Arch Linux

Seeing Arch Linux running so solidly in a VirtualBox virtual box has me contemplating whether I should have it installed on a real PC. Saying that, recent announcements regarding the implementation of GNOME 3 in Linux Mint have caught my interest even if the idea of using a rolling distribution as my main home operating system still has a lot of appeal for me. Having an upheaval come my way every six months when a new version of Linux Mint is released is the main cause of that.

While remaining undecided, I continue to evaluate the idea of Arch Linux acting as my main OS for day-to-day home computing. Towards that end, I have set up a working web server instance on there using the usual combination of Apache, Perl, PHP and MySQL. Of these, it was MySQL that went the least smoothly of all because the daemon wouldn’t start for me.

It was then that I started to turn to Google for inspiration and a range of actions resulted that combined to give the result that I wanted. One problem was a lack of disk space caused by months of software upgrades. Since tools like it in other Linux distros allow you to clear some disk space of obsolete installation files, I decided to see if it was possible to do the same with pacman, the Arch Linux command line package manager. The following command, executed as root, cleared about 2 GB of cruft for me:

pacman -Sc

The S in the switch tells pacman to perform package database synchronization while the c instructs it to clear its cache of obsolete packages. In fact, using the following command as root every time an update is performed both updates software and removes redundant or outmoded packages:

pacman -Syuc

So I don’t forget the needful housekeeping, this will be what I use in future with the y being the switch for a refresh and the u triggering a system upgrade. It’s nice to have everything happen together without too much effort.

To do the required debugging that led me to the above along with other things, I issued the following command:

mysqld_safe –datadir=/var/lib/mysql/ &

This starts up the MySQL daemon in safe mode if all is working properly and it wasn’t in my case. Nevertheless, it creates a useful log file called myhost.err in /var/lib/mysql/. This gave me the messages that allowed the debugging of what was happening. It led me to installing net-tools and inettools using pacman; it was the latter of these that put hostname on my system and got the MySQL server startup a little further along. Other actions included unlocking the ibdata1 data file and removing the ib_logfile0 and ib_logfile1 files so as to gain something of a clean sheet. The kill command was used to shut down any lingering mysqld sessions too. To ensure that the ibdata1 file was unlocked, I executed the following commands:

mv ibdata1 ibdata1.bad
cp -a ibdata1.bad ibdata1

These renamed the original and then crated a new duplicate of it with the -a switch on the cp command forcing copying with greater integrity than normal. Along with the various file operations, I also created a link to my.cnf, the MySQL configuration file on Linux systems, in /etc using the following command executed by root:

ln -s /etc/mysql/ my.cnf /etc/my.cnf

While I am unsure if this made a real difference, uncommenting the lines in the same file that pertained to InnoDB tables. What directed me to these were complaints from mysqld_safe in the myhost.err log file. All I did was to uncomment the lines beginning with “innodb” and these were 116-118, 121-122 and 124-127 in my configuration file but it may be different in yours.

After all the above, the MySQL daemon ran happily and, more importantly, started when I rebooted the virtual machine. Thinking about it now, I believe that was a lack of disk space, the locking of a data file and the lack of InnoDB support that was stopping the MySQL service from running.Running commands like mysqld start weren’t yielding useful messages so a lot of digging was needed to get the result that I needed. In fact, that’s one of the reasons why I am sharing my experiences here.

In the end, creating databases and loading them with data was all that was needed for me to start see functioning websites on my (virtual) Arch Linux system. It turned out to be another step on the way to making it workable as a potential replacement for the Linux distributions that I use most often (Linux Mint, Fedora and Ubuntu).

TypeError: unable to create a wrapper for GLib.Variant

A little while ago, I wrote a piece on here telling of how I got GNOME 3 installed an working on Linux Mint. However, I have discovered since that there was an Achilles heel in the approach that I had taken: using the ricotz/testing PPA so that I could gain additional extensions for use with GNOME Shell. If this was just a repository of GNOME Shell extensions, that would be well and good but the maintainer(s) also has a more cutting edge of GNOME Shell in there too. Occasionally, updates from ricotz/testing have been the cause of introducing rough edges to my desktop environment that have resolved themselves within a few hours or days. However, updates came through in the last few days that broke GNOME Tweak Tool. When I tried running it from the command line, all I got was a load of output that included the message that heads this posting and no window popping up that I could use. That made me see sense so I stopped living dangerously by using that testing repository. Apparently, there is a staging variant too but a forum posting elsewhere on the web has warded me off from that too.

Until I encountered the latter posting, I had not heard of the ppa-purge tool and it came in handy for ridding my system of all packages from the ricotz repository and replacing with with alternatives from more stable ones such as that from the gnome3-team. This wasn’t installed on my computer so I added it in the usual fashion by issuing the following command:

sudo apt-get install ppa-purge

Once that was complete, I executes the following command with the ricotz/testing repository still active:

sudo ppa-purge testing ricotz

Once that was complete and everything was very nicely automated too, GNOME Tweak Tool was working again as intended and that’s the way that I intend keeping things. Another function of ppa-purge is that it has excised any mention of the ricotz/testing repos from my system too so nothing more can come from there.

While I was in the business of stabilising GNOME Shell on my system, I decided to add in UGR too. First, another repository needed to be added as follows:

sudo add-apt-repository ppa:ubuntugnometeam/ppa-gen
sudo apt-get update

The next steps were to install UGR once that was in place so these commands were issued to do the job:

sudo apt-get dist-upgrade
sudo apt-get install ugr-desktop-g3
sudo apt-get upgrade

While that had the less desirable effect of adding games that I didn’t need and have since removed, it otherwise worked well and I now have a new splash screen at starting up and shutting down times for my pains. Hopefully, it will main that any updates to GNOME Shell that come my way should be a little more polished too. All that’s needed now is for someone to set up a dedicated PPA for GNOME Shell Extensions so I could regain drop down menus in the top panel for things such as virtual desktops, places and other handy operations that perhaps should have been in GNOME Shell from the beginning. However, that’s another discussion so I’ll content myself with what I now have and see if my wish ever gets granted.

Adding GNOME 3 to Linux Mint 11

On the surface of it, this probably sounds a very strange thing to do: choose Linux Mint because they plan to stick with their current desktop interface for the foreseeable future and then stick a brand new one on there. However, that’s what last weekend’s dalliance with Fedora 15 caused. Not only did I find that I could find my way around GNOME Shell but I actually got to liking it so much that I missed it on returning to using my Linux Mint machine again.

The result was that I started to look on the web to see if there was anyone else like me who had got the same brainwave. In fact, it was Mint’s being based on Ubuntu that allowed me to get GNOME 3 on there. The task could be summarised as involving three main stages: getting GNOME 3 installed, adding extensions and adding the Cantarell font that is used by default. After these steps, I gained a well-running GNOME 3 desktop running on Linux Mint and it looks set to stay that way unless something untoward has yet to emerge.

Installing GNOME 3

The first step is to add the PPA repository for GNOME 3 using the following command:

sudo add-apt-repository ppa:gnome3-team/gnome3

The, it was a case of issuing my usual update/upgrade command:

sudo apt-get update && sudo apt-get upgrade && sudo apt-get dist-upgrade

When that had done its thing and downloaded and installed quite a few upgrades along the way, it was time to add GNOME Shell using this command:

sudo apt-get install gnome-shell

When that was done, I rebooted my system to be greeted by a login screen very reminiscent of what I had seen in Fedora.While compiling this piece, I have seen that GNOME Session could need to be added before GNOME Shell but I do not recall doing so myself. Maybe dependency resolution kept any problems at bay but there weren’t any issues that I could remember beyond things not being configured as fully as I would have liked without further work. For sake of safety, it might be a good idea to run the following before adding GNOME Shell to your PC.

sudo apt-get install gnome-session && sudo apt-get dist-upgrade

Configuration and Customisation

Once I had logged in, the desktop that I saw wasn’t at all unlike the Fedora one and everything seemed stable too. However, there was still work to do before I was truly at home with it. One thing that was needed was the ever useful GNOME Tweak Tool. This came in very handy for changing the theme that was on display to the standard Adwaita one that caught my eye while I was using Fedora 15. Adding buttons to application title bars for minimising and maximising their windows was another job that the tool allowed me to do. The command to get this goodness added in the first place is this:

sudo apt-get install gnome-tweak-tool

The next thing that I wanted to do was go adding some extensions so I added a repository from which to do this using the command below. Downloading them via Git and compiling them just wasn’t working for me so I needed another approach.

sudo add-apt-repository ppa:ricotz/testing

With that is place, I issued the below commands to gain the Dock, the Alternative Status Menu and the Windows Navigator. The second of these would have added a shutdown option in the me-menu but it seems to have got deactivated after a system update. Holding down the ALT key to change the Suspend entry to Power off… will have to do me for now. Having the dock is the most important and that thankfully is staying the course and works exactly as it does for Fedora.

sudo apt-get install gnome-shell-extensions-dock
sudo apt-get install gnome-shell-extensions-alternative-status-menu
sudo apt-get install gnome-shell-extensions-windows-navigator

Adding Cantarell

The default font used by GNOME 3 in various parts of its interface is Cantarell and it was defaulting to that standard sans-serif font on my system because this wasn’t in place. That font didn’t look too well so I set to tracking the freely available Cantarell down on the web.  When that search brought me to Font Squirrel, I downloaded the zip file containing the required TTF files. The next step was to install them and, towards that end, I added Fontmatrix using this command:

sudo apt-get install fontmatrix

That gave me a tool with a nice user interface but I made a mistake when using it. This was because I (wrongly) thought that it would copy files from the folder that I told the import function to use. Extracting the TTF files to /tmp meant that would have had to happen but Fontmatrix just registered them instead. A reboot confirmed that they hadn’t been copied or moved at all and I had rendered the user interface next to unusable through my own folly; the default action in Ubuntu and Linux Mint is that files are deleted from /tmp on shutdown. The font selection capabilities of the GNOME Tweak Tool came in very handy for helping me converting useless boxes into letters that I could read. Another step was to change the font line near the top of the GNOME Shell stylesheet (never thought that CSS usage would end up in places like this…) so that Cantarell wasn’t being sought and text in sans-serif font replaced grey and white boxes. The stylesheet needs to be edited as superuser so the following command is what’s needed for this and, while I used sudo, gksu is just as useful here if it isn’t what I should have been using.

sudo gedit /usr/share/gnome-shell/theme/gnome-shell.css

Once I had extricated my system from that mess, a more conventional approach was taken and the command sequence below was what I followed, with extensive use of sudo to get done what I wanted. A new directory was created and the TTF files copied in there.

cd /usr/share/fonts/truetype
sudo mkdir ttf-cantarell
cd ttf-cantarell
sudo mv /tmp/*.ttf .

To refresh the font cache, I resorted to the command described in a tutorial in the Ubuntu Wiki:

sudo fc-cache -f -v

Once that was done, it was then time to restore the reference to Canterell in the GNOME Shell stylesheet and reinstate its usage in application windows using the GNOME Tweak Tool. Since then, I have suffered no mishap or system issue with GNOME 3. Everything seems to be working quietly and I am happy to see that replacement of Unity with the GNOME Shell will become an easier task in Ubuntu 11.10, the first alpha release of which is out at the time of my writing these words. Could it lure me back from my modified instance of Linux Mint yet? While I cannot say that I am sure of those but it certainly cannot be ruled out at this stage.

Why the manual step?

One of the consequences of buying a new camera is that your current photo processing software may not be fully equipped for the job of handling the images that it creates. This is a particular issue with raw image files and Adobe Photoshop Elements 5 was unable to completely handle DNG files made with my Pentax K10D until I upgraded to version 7. Yes, I do realise that upgrading camera should been in order but I only lost the white balance adjustments so I could with things as they until upgrading gained a more compelling case.

As things stood, Elements 7 was unable to import CR2 files from my Canon PowerShot G11 into the Organiser so it was off to the appropriate page on the Adobe website for a Camera Raw updater. I picked up the latest release of Camera Raw (5.6 at the time of writing) even though it was found in the Elements 8 category (don’t be put by this because release notes address the version compatibility question more extensively). Strangely, the updater doesn’t complete everything because you still need to copy Camera Raw.8bi from the zip archive and backup the original. Quite why this couldn’t have been more automated, even with user prompts for file names and locations, is beyond me but that is how it is. However, once all was in place, CR2 files were handled by Elements without missing a beat.

Command Line Software Management

One of the nice things about a Debian-based Linux distribution is that it is easy to pull a piece of software onto your system from a repository using either apt-get or aptitude. Some may prefer to have a GUI but I find that the command line offers certain extra transparency that stops the “what’s it doing?” type of question. that’s never to say that the GUI-based approach hasn’t a place and I only go using it when seeking out a piece of software without knowing its aptitude-ready name. Interestingly, there are signs that Canonical may be playing with the idea of making Ubuntu’s Software Centre a full application management tool with updates and upgrades getting added to the current searching, installation and removal facilities. That well may be but it’s going to take a lot of effort to get me away from the command line altogether.

Fedora and openSUSE have their software management commands too in the shape of yum and zypper, respectively. The recent flurry of new operating system releases has had me experimenting with both of those distros on a real test machine. As might be expected, the usual battery of installation, removal and update activities are well served and I have been playing with software searching using yum too. What has yet to mature is in-situ distribution upgrading à la Ubuntu. In principle, it is possible but I got a black screen when I tried moving from openSUSE 11.1 to 11.2 within VirtualBox using instructions on the openSUSE website. Not wanting to wait, I reached for a Live CD instead and that worked a treat on both virtual and real machines. Being in an experiment turn of mind, I attempted the same to get from Fedora 11 to the beta release of its version 12. A spot of repository trouble got me using a Live CD in its place. You can perform an in-situ upgrade from a full Fedora DVD but the only option is system replacement when you have a Live CD. Once installation is out of the way, YAST can be ignored in favour of zypper and yum is good enough that Fedora’s GUI-using alternative can be ignored. It’s nice to see good transparent ideas taking hold elsewhere and may make migration between distros much easier too.

Out of memory at line: 56

This is an error that I have started to see a lot in the last few weeks. First, it was with Piwik and latterly with WordPress.com Stats. For the record, I have never seen it on up to date systems but always with IE6 and at page unloading time. The CPU usage hits 100% before the error is produced and that has had me blaming JavaScript in error; it isn’t the cause of all ills. In fact, the cause seems to be a bug in a certain release of Adobe Flash 9 but I am of the opinion that the inclusion of certain features in a Flash movie are needed to trigger it too. I don’t have the exact details of this but WordPress.com Stats worked without fault until a recent update and that is what is making me reach the conclusion that I have. That observation is making me wonder whether we are coming to a point where Flash compatibility is something that needs to factored into the use of the said technology in a website or web application. Updating Flash will solve the problem on the client but it might be better if it wasn’t triggered on the server side either.

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