Archive for Software

ERROR: Ambiguous reference, column xx is in more than one table.

May 5, 2012 No comments

Sometimes, SAS messages are not all that they seem and a number of them are issued from PROC SQL when something goes awry with your code. In fact, I got a message like the above when ordering the results of the join using a variable that didn’t exist in either of the datasets that were joined. This type of thing has been around for a while (I have been using SAS since version 6.11 and it was there then) and it amazes me that we haven’t seen a better message in more recent versions of SAS; it was SAS 9.2 where I saw it most recently.

proc sql noprint;
select a.yy, a.yyy, b.zz
from a left join b
on a.yy=b.yy
order by xx;
quit;

Programming, Software

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Changing from Nouveau to Nvidia Graphics Drivers on Linux Mint Debian Edition 64-bit

April 22, 2012 One comment

One way of doing this is to go to the Nvidia website and download the latest file from the relevant page on there. Then, the next stage is to restart your PC and choose rescue mode instead of the more usual graphical option. This drops you onto a command shell that is requesting your root password. Once this is done, you can move onto the next stage of the exercise. Migrate to the directory where the *.run file is located and issuing a command similar to the following:

bash NVIDIA-Linux-x86_64-295.40.run

The above was the latest file available at the time of writing so the name may have changed by the time that you read this. If the executable asks to modify your X configuration file, I believe that the best course is to let it do that. Editing it yourself or running nvidia-xconfig are alternative approaches if you so prefer.

Proprietary Nvidia drivers are included the repositories for Linux Mint Debian Edition so that may be a better course of action since you will get updates through normal system update channels. Then, the course of action is to start by issuing the following installation comands:

sudo apt-get install module-assistant
sudo apt-get install nvidia-kernel-common
sudo apt-get install nvidia-glx
sudo apt-get install kernel-source-NVIDIA
sudo apt-get install nvidia-xconfig

Once those have completed, issuing the following in turn will complete the job ahead of a reboot:

sudo m-a a-i nvidia
sudo modprobe nvidia
sudo nvidia-xconfig

If you reboot before running the above like I did, you will get a black screen with a flashing cursor instead of a full desktop because X failed to load. Then, the remedy is to reboot the machine and choose the rescue mode option, provide the root password and issue the three commands (at this point, the sudo prefix can be dropped because it’s unneeded) then. Another reboot will see order restored and the new driver in place. Running the following at that point will do a check on things as will be the general appearance of everything:

glxinfo | grep render

Graphics, Hardware, Linux, Software, Video

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Synchronising package selections between Linux Mint and Linux Mint Debian Edition

April 18, 2012 No comments

To generate the package list on the GNOME version of Linux Mint, I used the Backup Tool. It simply was a matter of using the Backup Software Selection button and telling it where to put the file that it generates. Alternatively, dpkg can be used from the command line like this:

sudo dpkg –get-selections > /backup/installed-software.txt

After transferring the file to the machine with Linux Mint Debian Edition, I tried using the Backup Tool on there too. However, using the Restore Software Selection button and loading the required only produced an irrecoverable error. Therefore, I set to looking around the web and found a command line approach that did the job for me.

The first step is to load the software selection using dpkg by issuing this command (it didn’t matter that the file wasn’t made using the dpkg command though I suspect that’s what the Linux Mint Backup Tool was doing that behind the scenes):

sudo dpkg –set-selections < /backup/installed-software.txt

Then, I started dselect and chose the installation option from the menu that appeared. First time around, it fell over but trying again was enough to complete the job. Packages available to the vanilla variant of Linux Mint but not found in the LMDE repositories were overlooked as I had hoped and installation of the extra packages had no impact on system stability either.

sudo dselect

Apparently, there is an alternative to using dselect that is based on the much used apt-get command but I didn’t make use of it so cannot say more:

sudo apt-get dselect-upgrade

All that I can say is that the dpkg/dselect combination did what I wanted so I’ll keep them in mind if ever need to synchronise software selections between two Debian-based distributions in the future again. The standard edition of Linux Mint may be based on Ubuntu rather than Debian but Ubuntu is itself based on Debian so the description holds here.

Linux, Software

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Uninstalling VirtualBox Guest Additions on a Linux Guest OS

April 8, 2012 No comments

Within the last few days, I updated my Linux Mint Debian Edition virtual machine installation to Update 4. Between not following the instructions so closely and problems with the update server, a re-installation preceded the update itself. When all was done, no desktop environment appeared and issuing the startx command revealed that it was one of the VirtualBox drivers that was the cause of the problem. With my being unable to see any files on the VirtualBox virtual CD, something else needed doing and the executing following command (replacing [VboxAddonsFolder] with VBoxGuestAdditions-4.1.12 in my case but it is different for each VirtualBox version) resolved the situation:

/opt/[VboxAddonsFolder]/uninstall.sh

When it was complete, a scrambled desktop began to appear so a reboot was in order to set things to rights. Then, I could set to looking at what Update 4 had brought to Linux Mint Debian Edition.

Linux, Software, Virtualisation

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Calculating geometric means using SAS

March 19, 2012 No comments

Recently, I needed to calculate geometric means after a break of a number of years and ended racking a weary brain until it was brought back to me. In order that I am not in the same situation again, I am recording it here and sharing it always is good too.

The first step is to take the natural log (to base e or the approximated irrational value of the mathematical constant, 2.718281828) of the actual values in the data. Since you cannot have a log of zero, the solution is either to exclude those values or substitute a small value that will not affect the overall result as is done in the data step below. In SAS, the log function uses the number e as its base and you need to use the log10 equivalent when base 10 logs are needed.

data temp;
set temp;
if result=0 then _result=0.000001;
else _result=result;
ln_result=log(_result);
run;

Next, the mean of the log values is determined and you can use any method of doing that so long as it gives the correct values. PROC MEANS is used here but PROC SUMMARY (identical to MEANS except it defaults to data set creation while that generates output by default; because of that, we need to use the NOPRINT option here), PROC UNIVARIATE or even the MEAN function in PROC SQL.

proc means data=temp noprint;
output out=mean mean=mean;
var ln_result;
run;

With the mean of the log values obtained, we need to take the exponential of the obtained value(s) using the EXP function. This returns values of the same magnitude as in the original data using the formula emean.

data gmean;
set mean;
gmean=exp(mean);
run;

Programming, Software

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Creating placeholder graphics in SAS using PROC GSLIDE for when no data are available

March 18, 2012 One comment

Recently, I found myself with a plot to produce but there were no data to be presented so a placeholder output is needed. For a lisitng or a table, this is a matter of detecting if there are observations to be listed or summarised and then issuing a placeholder lisitng using PROC REPORT if there are no data available. Using SAS/GRAPH, something similar can be acheived using one of its curiosities.

In the case of SAS/GRAPH, PROC GSLIDE looks like the tool to user for the same purpose. The procedure does get covered as part of a SAS Institute SAS/GRAPH training course but they tend to gloss over it. After all, there is little reason to go creating presentations in SAS when PowerPoint and its kind offer far more functionality. However, it would make an interesting tale to tell how GSLIDE became part of SAS/GRAPH in the first place. Its existence makes me wonder if it pre-exists the main slideshow production tools that we use today.

The code that uses PROC GSLIDE to create a placeholder graphic is as follows (detection of the number of observations in a SAS dataset is another entry on here):

proc gslide;
note height=10;
note j=center “No data are available”;
run;
quit;

PROC GSLIDE is one of those run group procedures in SAS so a QUIT statement is needed to close it. The NOTE statements specify the text to be added to the graphic. The first of these creates a blank line of the required height for placing the main text in the middle of the graphic. It is the second one that adds the centred text that tells users of the generated output what has happened.

Programming, Software

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