s indicated in the previous post, sometimes it is necessary to use old versions of a particular package which is not available from the repositories. The screenshot below shows what’s available in Fedora as far as Octave is concerned.

It would be extremely valuable to have links to alternative repositories or even Web sites that offer previous builds of the software, even if these are not “official” and thus less safe. It is not ideal for many different reasons, but it can prevent people from searching the Web for other RPMs that come from entirely untrusted sources.

Fedora is not the problem here, but a constructive suggestion such as this one may become a selling point to some users.

Y EARLIER experiences with Konqueror go back to ~2002 when I tried it at work under Mandrake, around the early versions of KDE3 or later KDE2. Konqueror had many menu options and was daunting in some ways compared to Netscape and Mozilla. In KDE 3.1 Konqueror had acceptance problems among Web sites that were simply IE-centric or IE- and Netscape-centric. This was not a problem in Konqueror itself, but it made life a little harder for Konqueror users like myself. I only moved to Firefox some time in 2004 and it is still my Web browser of choice, having tested Chromium and some other browsers for a while (they lack plugins).

Anyway, under Fedora 14 I am attempting to use Konqueror exclusively and it’s generally a pleasant experience. After over a week of use I’ve only experienced two issues; one is when opening a PDF which Okular tried to embed within the Web page/rendering frame (this is easily solvable by opening the PDFs in an external application like the excellent Okular); the second issue is repeatable and reproducible crashes under WordPress’ media management menu. It’s a Web application-specific issue and debugging would be needed.

Workarounds are quite simple to find and the general experience working with Konqueror is finally quite pleasant (I tried Konqueror exclusively for about half a week in KDE 4.3 but eventually gave up). Speed is not great and there is room for improvement, but for general-purpose light usage Konqueror would fit most people’s needs. Some time later this month I will write about KDE 4.5 as a whole.

few days ago I started working with Fedora 14. So far, so good, at least as far as the desktop machine goes (a laptop is another story and Kubuntu runs fine on another desktop). Something has just happened in Fedora which never happened to me before. Kate (an editor) got stuck and its memory (RAM) consumption went up through the roof to over 1.5 GB, so obviously it froze the system for a while. The process needed to be forcibly killed.

Now, it’s not entirely clear what happened there (maybe a program bug), but this is unusual and it looks bad for Fedora or for KDE (or the combination in Fedora 14 KDE spin). What did happen is that SELinux came up with an error implying that it stood in Kate’s way and maybe it’s partly responsible for this type of behaviour. It yielded the following error, implying that it was trying to help when in fact it seemed like it only stood in the way.

Summary:

SELinux is preventing /usr/bin/kate (deleted) “mmap_zero” access on <Unknown>.

Detailed Description:

SELinux denied access requested by kate. The current boolean settings do not
allow this access. If you have not setup kate to require this access this may
signal an intrusion attempt. If you do intend this access you need to change the
booleans on this system to allow the access.

Allowing Access:

Confined processes can be configured to run requiring different access, SELinux
provides booleans to allow you to turn on/off access as needed. The boolean
mmap_low_allowed is set incorrectly.
Boolean Description:
Control the ability to mmap a low area of the address space, as configured by
/proc/sys/kernel/mmap_min_addr.

Fix Command:

# setsebool -P mmap_low_allowed 1

Additional Information:

Source Context unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1
023
Target Context unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1
023
Target Objects None [ memprotect ]
Source kate
Source Path /usr/bin/kate (deleted)
Port &ltUnknown>
Host blueberry
Source RPM Packages
Target RPM Packages
Policy RPM selinux-policy-3.9.7-3.fc14
Selinux Enabled True
Policy Type targeted
Enforcing Mode Enforcing
Plugin Name catchall_boolean
Host Name blueberry
Platform Linux blueberry 2.6.35.6-45.fc14.i686 #1 SMP Mon
Oct 18 23:56:17 UTC 2010 i686 i686
Alert Count 112
First Seen Sun 14 Nov 2010 09:35:01 AM GMT
Last Seen Sun 14 Nov 2010 09:35:17 AM GMT
Local ID 4d9759c9-e672-475d-bf61-151d1688909a
Line Numbers

Raw Audit Messages

node=blueberry type=AVC msg=audit(1289727317.378:856): avc: denied { mmap_zero } for pid=1880 comm=”kate” scontext=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023 tcontext=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023 tclass=memprotect

node=blueberry type=SYSCALL msg=audit(1289727317.378:856): arch=40000003 syscall=192 success=no exit=-13 a0=0 a1=100000 a2=0 a3=4022 items=0 ppid=1629 pid=1880 auid=500 uid=500 gid=500 euid=500 suid=500 fsuid=500 egid=500 sgid=500 fsgid=500 tty=(none) ses=1 comm=”kate” exe=2F7573722F62696E2F6B617465202864656C6574656429 subj=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023 key=(null)

For years I’ve been working with no data loss, but this time I had to revert back to a previously-saved version of a document I worked on and then rewrite bits of it. Perhaps I had enough confidence in the system to only hit save (CTRL+S) once in a very long time. This experience has taught me to save my work more often but more importantly it showed that Fedora can act rather bizarrely where Kubuntu never did. As a result of this behaviour I was unable to save my work. SELinux implies there was an “attack” on the system, but obviously there was not.

T HAS been a while since I last did a comprehensive survey of DICOM-related software and since I am ditching MATLAB (in the quest for Free software-only research) I decided to review or at least check out what’s available at the end of 2010. Other people may find this handy.

DICOM is notorious for being the standard that’s not quite the standard and is actually somewhat proprietary and controlled by one entity. As someone pointed out the other day, DICOM is considered “extensible”, which implies that the usual type of format ‘bastardisation’ will always occur. It’s just an inconsistent data format as someone warned, so some software would cough at it and sometimes manage to salvage some data. According to Wikipedia, some tagging of the image/s is accompanied by data fields like:

Let us say that we are more interested in the raw image data and not so much in the metadata. If that’s the case, batch conversion to a more manageable format is worthwhile. Here is the command-line converter that I use (some are for Windows only and they are proprietary) and some other options can be found on the Web through directories. There are also good software resources on scientific data formats and there is radiology CEU information regarding PACS and DICOM viewers. There is actually far more choice out there than there was a few years ago. For GNU/Linux and Free software proponents there is no lack or deficiency, either.

feel as though I must apologise for hasty remarks that I made in yesterday’s audiocast when we discussed GNU Octave (so I posted an update). I was basing my assessment on a very old experience and my understanding, as I found it out today, is that more and more MALTAB users consider moving to Octave due to the increasing cost of MATLAB. Another person whose background is in Mathematica taught me some more about the state of Octave. To quote from IRC:

*Quadrescence (~Quad@unaffiliated/quadrescence) has joined #boycottnovell-social		Nov 01 22:25
FurnaceBoy	Quadrescence: wb // schestowitz look who’s here	Nov 01 22:26
Quadrescence	hi	Nov 01 22:26
schestowitz	Hey	Nov 01 22:28
schestowitz	I was contacted by octave dev	Nov 01 22:28
schestowitz	Did you use it?	Nov 01 22:28
schestowitz	I just need to be able to deal with DICOM in it	Nov 01 22:28
schestowitz	Problem is, octave might not have good 3d visualisation tools	Nov 01 22:28
Quadrescence	I am pretty sure Octave just uses gnuplot	Nov 01 22:29
schestowitz	sjvn: “@sjvn it’s the pet peeve of mine I told you about before. Some colleagues like Gralla and pro-Windows showing up and reducing signal for me.”	Nov 01 22:29
schestowitz	Quadrescence: yeah	Nov 01 22:29
schestowitz	which is rather primitive compared to binary junk	Nov 01 22:30
schestowitz	So I need to use the junk	Nov 01 22:30
Quadrescence	schestowitz: What do you mean?	Nov 01 22:30
schestowitz	“@sjvn it’s the pet peeve of mine I told you about before. Some colleagues like Gralla and pro-Windows showing up and reducing signal for me.”	Nov 01 22:30
schestowitz	I think it’s not true. He still boosts Windows (gralla)	Nov 01 22:31
schestowitz	“@schestowitz thanks anyway. I already knew about octave-bioinfo, but it’s functionality is quite limited…”	Nov 01 22:31
schestowitz	Quadrescence: re mathematica	Nov 01 22:31
schestowitz	You though of leaving it?	Nov 01 22:31
schestowitz	maple and matlab are similar	Nov 01 22:31
Quadrescence	schestowitz: Sorry, I don’t know what you mean	Nov 01 22:33
Quadrescence	schestowitz: Are you saying gnuplot is primitive compared to mathematica/maple/matlab?	Nov 01 22:34
schestowitz	for plotting I think it’s lacking in comparison	Nov 01 22:35
schestowitz	The octave guy admitted it	Nov 01 22:35
schestowitz	I work with images a lot	Nov 01 22:35
schestowitz	for just plain stats I could use octave	Nov 01 22:35
Quadrescence	Actually I’d say gnuplot is rather phenomenal.	Nov 01 22:35
FurnaceBoy	pics or gtfo	Nov 01 22:36
Quadrescence	An alternative to gnuplot would be to use Sage: http://i.imgur.com/71Hr3.png	Nov 01 22:36
TechrightsBot-sc	Title: Not a web page! Aborting image/png type .::. Size~: 0 KB	Nov 01 22:36
Quadrescence	P and Q are plots. To plot them together, just do P+Q	Nov 01 22:36
Quadrescence		Nov 01 22:36
schestowitz	Nice	Nov 01 22:36
schestowitz	Maybe it has improved	Nov 01 22:36
Quadrescence	I don’t think that is gnuplot tho	Nov 01 22:36
Quadrescence	In fact, I know it isn’t	Nov 01 22:36
MinceR	gnupowder plot	Nov 01 22:37
schestowitz	gnuspamassassin plot	Nov 01 22:37
Quadrescence	gnuplot is still great: http://gnuplot.sourceforge.net/demo_svg/singulr.html	Nov 01 22:38
TechrightsBot-sc	Title: gnuplot demo script: singulr.dem  .::. Size~: 8.92 KB	Nov 01 22:38
Quadrescence	http://gnuplot.sourceforge.net/demo_svg/contours.html	Nov 01 22:39
TechrightsBot-sc	Title: gnuplot demo script: contours.dem  .::. Size~: 10.67 KB	Nov 01 22:39
Quadrescence	stuff in general: http://gnuplot.sourceforge.net/demo_svg/	Nov 01 22:39
TechrightsBot-sc	Title: Demo scripts for SVG terminal in gnuplot version 4.4 .::. Size~: 5.63 KB	Nov 01 22:39
Quadrescence	opacity: http://gnuplot.sourceforge.net/demo/transparent_solids.2.png	Nov 01 22:40
TechrightsBot-sc	Title: Not a web page! Aborting image/png type .::. Size~: 0 KB	Nov 01 22:40
Quadrescence	Anyway, the best thing about gnuplot is that it’s incredibly fast/lightweight.	Nov 01 22:41
Quadrescence	Mathematica has a tendency of blowing 2GB of RAM just to get a decent surface plot	Nov 01 22:41
Quadrescence	MathGL is an incredible open source library for making absolutely spectacular plots: http://mathgl.sourceforge.net/pictures.html	Nov 01 22:42
TechrightsBot-sc	Title: MathGL – pictures .::. Size~: 4.34 KB	Nov 01 22:42
Quadrescence	*and* you can use it with Octave	Nov 01 22:43
FurnaceBoy	Quadrescence: that is impressive (the svg stuff)	Nov 01 22:53
*FurnaceBoy lieks svg		Nov 01 22:53
schestowitz	abeNd-org: syntax compatible?	Nov 01 22:56
schestowitz	Quadrescence ^^	Nov 01 22:56
schestowitz	Could I attempt to run old matlab programs with gnuplot and octave?	Nov 01 22:57
schestowitz	FurnaceBoy: <SFT have VML	Nov 01 22:57
schestowitz	SVG scares them cause it ain’t THEIRS.	Nov 01 22:57
schestowitz	*MSFT I meant	Nov 01 22:57
FurnaceBoy	schestowitz: fine , let it scare them	Nov 01 22:58
Quadrescence	schestowitz: it is mostly compatible	Nov 01 22:59
*Ender2070 (~Ender2070@CPE00222d6e3608-CM00222d6e3605.cpe.net.cable.rogers.com) has joined #boycottnovell-social		Nov 01 23:04
schestowitz	FurnaceBoy: they ‘joined’ this year	Nov 01 23:04
schestowitz	Only to keep pushing VML	Nov 01 23:04
schestowitz	They need to intervene in the competition too	Nov 01 23:04
schestowitz	To bend it	Nov 01 23:05
schestowitz	See MSODF for example	Nov 01 23:05
FurnaceBoy	bend -> break.	Nov 01 23:05
schestowitz	Microsoft fragmented ODF	Nov 01 23:05
FurnaceBoy	hehe	Nov 01 23:05
FurnaceBoy	tried w/ java	Nov 01 23:05
FurnaceBoy	+ html	Nov 01 23:05
schestowitz	got sued	Nov 01 23:05
schestowitz	They try again now	Nov 01 23:05
schestowitz	AZune [sic] cloud	Nov 01 23:05
FurnaceBoy	yes, they only have one trick	Nov 01 23:05
schestowitz	Inviting Java dvs	Nov 01 23:05
schestowitz	*devs	Nov 01 23:05

It turns out that my employer may also allow me to move from MALTAB to Octave, thus using only Free software in my research. In fact, I’m installing Octave at this very moment.

“No episode number, this isn’t a soap opera”

Direct download as Ogg (1:09:43, 38 MB) | Direct download as MP3

Summary: TechBytes audiocast opens with a pre-launch episode where we mostly explore the terrain

HIS IS OUR test episode, a pilot so to speak. We did it all in one go (over an hour) without any notes or scripts and it is not edited. We hope that it’ll be acceptable and in our next episode (probably in November) we’ll use experience from this first run and also refine by doing some planning, then editing. Please treat it as a beta episode if it helps and we thank you for listening.

As embedded (HTML5):

Download:

Cross-posted in Techrights

Summary: Techrights is in the December 2010 issue of Linux Format Magazine

OR THOSE who want to know more about the history of Techrights, there is a new article in the December 2010 issue of Linux Format. The content is available only to subscribers. We thank Linux Format for generally being quite supportive over the years. There are some circles that are hostile towards us and upon closer inspection it usually turns out that they also oppose GNU/Linux and/or Free software, in which case this hostility may actually be indicative of the idea that we are effective. Techrights is still a group effort and achievements that are being made are communal, not personal. Thanks to all those who recommend the site to friends and colleagues, thus ensuring the continued growth of readership and input that accompanies it (recently we have been getting translations too).