Request: SciPlore 15 beta [FILLED]

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Puppyt
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Request: SciPlore 15 beta [FILLED]

#1 Post by Puppyt »

About a year ago, robwoj44 very kindly provided a pet for SciPlore 10 beta - formerly known as "FreeMind Scholar", a software package that combined mind-mapping with pdf management AND bibliography creation for students and researchers alike (http://www.murga-linux.com/puppy/viewtopic.php?t=57307).

The pet hasn't been updated with all the improvements listed here http://www.sciplore.org/software/sciplo ... /#download, and I am requesting that someone please accept the challenge to develop an updated pet or sfs for the Puppy community. (And me, plus a bunch of uni students I hope to lure off Vista and Win7...)

I unfortunately have problems with robwoj44's earlier pet as it failed to integrate fully with PDF and image files in a way I outlined in my original request here:http://www.murga-linux.com/puppy/viewtopic.php?t=56136. I wonder whether these problems I encountered remain Puppy-specific, or have been solved in the later upgrades of SciPlore.

Thanks very much for your attention,

Puppyt


UPDATE: THREAD SUMMARY 2Aug '11
I think I can safely call this request "FILLED".
Many Thanks to Geoffrey and Ariel for their impetus to get this over the line. SciPlore (FreeMind Scholar) is just about to evolve into FreePlane-based "Docear" that hopefully won't encounter the XDG-open problem in Puppy. SciPlore in Puppy however will still require some manual massage to have it working to the user's requirements. Here's the copy of my openfile.sh:

Code: Select all

#!/bin/bash
#this script opens files within freemind-0.9.0
#to use install the script in /usr/bin
#open freemind and go to Tools>Preferences>HTML menu
#in Defaul Browser Command Other Os, insert this command: openfile.sh {0}
#save
#quit freemind and launch it again
#
#you can add other programs provided you add the extension of the file you want to launch (last 3 characters)



ext=`echo "$@" | sed 's/.*\(...\)$/\1/'`

if [ "$ext" == doc ] ; then abiword "$@"
   elif [ "$ext" == txt ] ; then abiword "$@"
   elif [ "$ext" == tml ] ; then firefox "$@"
   elif [ "$ext" == abw ] ; then abiword "$@"
   elif [ "$ext" == pdf ] || [ "$ext" == PDF ] ; then evince "$@"
   # elif [ "$ext" == pdf ] || [ "$ext" == PDF ] ; then FoxitReader "$@"
   elif [ "$ext" == jpg ] || [ "$ext" == JPG ] ; then viewnior "$@"
   # elif [ "$ext" == jpg ] || [ "$ext" == JPG ] ; then evince "$@"

fi
I've commented out the jpg option for eVince - it can read a wide range of file formats - and it works here as does Viewnior. It also opens PDF's correctly and very rapidly. I would prefer Foxit Reader as apparently SciPlore retains user's highlighting and annotations made to any pdf in Foxit Reader. In my findings it just starts Foxit, doesn't open the pdf, and hence is commented out here. I'll post any other problem I might find in the next few days of use.
:D

[Test environment: using pemasu's Polarpup-003, Woof, kernel 2.6.39-3(i686); Geoffrey's SciPlore 15beta pet; Ariel's openfile and cgj-jre-4-4-4-3-lucid pets (latter might not be required), with this added to my etc/profile file:

Code: Select all

export JAVA_HOME=/usr/lib/jvm/java-6-openjdk
export PATH=$PATH:/usr/lib/jvm/java-6-openjdk/jre/bin
Plus, ttuuxx's jre-6u26-1-i386 and evince-2.30.3-i386 pets; and the FoxitReader-1.1-lucid pet downloaded via PPM]
Last edited by Puppyt on Thu 04 Aug 2011, 02:15, edited 2 times in total.
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#2 Post by Geoffrey »

I posted a download for it here, hope it's what you want.
http://www.murga-linux.com/puppy/viewtopic.php?t=57307

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#3 Post by Puppyt »

WOW!
Thanks Geoffrey - (and you're only an Aussie stones-throw away) I'll test this in Lucid puplets with great interest indeed - this is fabulous,
Cheers!
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#4 Post by Geoffrey »

Puppyt wrote:WOW!
Thanks Geoffrey - (and you're only an Aussie stones-throw away) I'll test this in Lucid puplets with great interest indeed - this is fabulous,
Cheers!
No worries mate,

if you need a sfs of it let me know, it will be "SciPlore_MindMapping_Linux-015b_525.sfs" and I'll upload it for you.

I'm sure others would like to give it a try, it looks interesting, wonder what is does, :? lol

Geoffrey

PS if you want it in a different menu just state which one, I just thought docs was the appropriate place

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#5 Post by Puppyt »

Cheers Geoffrey -
I've loaded your pet into a frugal-install Lucid 5.20 experimental project I have going on my desktop (2.6.33.2 (i686) kernel, 2.4GHz Celeron, 2Gb RAM). I have CowLog1.1 deb, KDE3.5, Kommander, R+Rcmdr, Java 1.6.0_22 all working happily here but importantly for SciPlore integration: AbiWord 2.8.6, Viewnoir 1.0, mpaint 3.34.59, and ePDFView 0.1.7. So I think that my foundations are basically sound (well - not mine, but you know what I mean).
Unfortunately SciPlore15 still gives me the same problems as I encountered with robwoj44's version, as I outlined earlier. With a *little* more Puppy/Linux experience under my belt I've had a bit of a brainstorm into fixing the possible problem with SciPlore's integration with Puppy. Here's the behaviour:-
1) I can drag all types of documents (doc, rtf, jpg, pdf) straight onto wherever I like to create mindmap structures that are completely editable (i.e., move and attribute details to "nodes" - data and/or links to files) just as the SciPlore developers intended.
2) I can create a "monitored folder" containing a library of PDF files from within SciPlore - ALL the bookmarks/subheadings to ALL the files available are generated swiftly and clearly displayed in an automatically-generated map. Badda-bing, badda-boom - worth the price of admission.
3) I haven't tried generating BibTex keys as I haven't got SciPlore's modified JabRef for extracting PDF metadata - baby steps first...
4) Click on the mindmap nodes with DOC or RTF files linked to them, and AbiWord opens those files nearly instantaneously. Wheee!

Here's where I get 'fails":
5) Click on an image file (jpg) and mtPaint baulks at opening the file correctly ("Cannot open file" error message) from WITHIN SciPlore - even though the file can be dragged from ROX into mtPaint and open correctly from outside SciPlore,
and;
6) Click on a PDF file and ePDFViewer gives me an "Encrypted Document: This document is encrypted and can't be accessed. Please enter the document's password:". The document is not actually encrypted and opens fine from outside SciPlore.

So where I think there is a problem is with SciPlore's automatic attribution of file types and applications on installation. Maybe ePDFView has inherent problems in Puppy 5 (?) and if I point SciPlore to another app like evince2, PDFedit etc I might have the files accessed properly from within SciPlore. Same with a re-directed image app instead of mtPaint, perhaps. Trouble is, I don't know if this is the solution, even if I had the nous to find out where to make the changes.
Any suggestions from any Puppians to solving this problem gratefully received,
Cheers!

PS Actually Geoffrey, I think that having SciPlore within the 'Document/Publishing' category is perfect, given the publishing aims of the software. Good choice!
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#6 Post by Puppyt »

Quick addition to my point '6' above - I just went to
~/Choices/MIME-types
and clicked on "application_pdf" in an attempt to check out the default behaviour. I got the same "Encrypted Document" dialogue as reported earlier - even though no document was in the process of being opened. Hmmmmm. But I still can't see the wood for the trees - will somebody explain this to me or point me to a reference thread in the forum? Getting closer to solving the problem, I feel.
("application_jpeg" tries to open Viewnoir rather than mtPaint. Confused again.)
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#7 Post by Geoffrey »

Puppyt wrote:Quick addition to my point '6' above - I just went to
~/Choices/MIME-types
and clicked on "application_pdf" in an attempt to check out the default behaviour. I got the same "Encrypted Document" dialogue as reported earlier - even though no document was in the process of being opened. Hmmmmm. But I still can't see the wood for the trees - will somebody explain this to me or point me to a reference thread in the forum? Getting closer to solving the problem, I feel.
("application_jpeg" tries to open Viewnoir rather than mtPaint. Confused again.)
I just had a look at the problem with pdf and tried this, in the " application_pdf" located in ~/Choices/MIME-types

try editing the script to read

Code: Select all

#! /bin/sh
#exec epdfview "$1"
exec epdfview "$@"
that seems to work, don't get the "Encrypted Document" dialogue.

As for " Viewnoir rather than mtPaint " that is determined by defaultimageeditor and defaultimageviewer in /usr/local/bin/

That might give you a clue to fixing your problem.

Geoffrey

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#8 Post by Puppyt »

Thanks again Geoffrey,
I tried your script change, and then I changed the default pdf viewer to "PDFedit" (I tried installing "evince" but I think the latest pet is for Puppy 4.3.1 - loads of missing libraries it seems, and no loading. The latest [EDIT] FOXIT READER-lucid pet also failed to install properly). Attempted PDFedit with both "$1" and "$@", and even uninstalled and then re-installed your SciPlore pet. PDFs in SciPlore still reverted to ePDFView and 'encrypted'. But I think that we're on the right track. I'm not happy with my base build and will try another kernel in the 5.2.5 area, I think - with no default PDF viewer present before I install SciPlore, and see how that goes. Just out of interest, what sort of behaviour do you get with different filetypes in your SciPlore mindmaps, if you've tried?
Thanks,
Puppyt
Last edited by Puppyt on Sun 15 May 2011, 00:46, edited 1 time in total.
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#9 Post by Geoffrey »

Puppyt,

Ive tried it but I can't get it to view anything, I'm using it in 525

like you said I drag files to it and and create a map but that's about as far as it go's.

when I try clicking on a file to view it I keep getting error box's saying the that it can't find the file at that particular path.

It's got me beat, though it would be good to get it working, after reading about what it does I would find it very useful.

hopefully someone will work out what the problem is, it's beyond me, I'm not that clue'y. :?

Geoffrey

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#10 Post by Geoffrey »

Puppyt,

I had a look around and came across Compendium, I ran it, looks good, whether its the same but in a different way to SciPlore I really don't know
but it seems to work without fault, I tried it with a pdf , svg not a problem,
it asks you what you want to open them with so it looks a lot easier to set up.

It has video help tutorials and heaps of support by the look of it, it don't look to shabby either, nice GUI would run rings around SciPlore
though it would take a bit of getting use to.

check it out here http://compendium.open.ac.uk/institute/
I downloaded the Compendium 2.0 Beta 1
you just have to give a name and email address to get the download link

seeing that I have it already downloaded I could make a pet.
the pet would be 37meg when extracted it's 77meg

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#11 Post by Puppyt »

Thanks, Geoffrey, for taking the extra time to check that out -
I had a miserable time too with other 5.2 bases, barebone-ish without a default PDF viewer installed. AbiWord still came up trumps as a correctly-linked doc or rtf file/node within SciPlore, but I was getting different "Cannot link" messages for images and pdfs - probably similar path error dialogue as you saw with yours, including some "%" codes and whatnot. My eyes tend to glaze over when I see that sort of gobbledygeek - I didn't take accurate notes at the time. I still dream of getting it working though, perhaps in a fully-fledged pup like LightHouse 5.03, or Bruno (with the Wine option for SciPlore.exe still possible) - or even TEENpup2010minbeta (4.31: http://murga-linux.com/puppy/viewtopic.php?t=52735) - firstly to get it going as Puppy proof-of-principle, and then to work back to what is missing with the linkage structure and where to correct it for a barebones 5.2x. Technological troglodyte that I am, there must be a logic under it even I can understand...(?)
There are still some "official" avenues left for me to try - from SciPlores website:
Linux

If you are experiencing difficulties in starting the software you may try running "/lib/freemind.jar". FreeMind's special help page for Linux [http://freemind.sourceforge.net/wiki/in ... d_on_Linux] might also be useful for you.
And, I've been on their mailing list for a little over a year now. Perhaps I should ask them directly for hints :) And another obvious test is to load up the FreeMind pet posted elsewhere on the Puppy forums, and see how that one behaves (but without the pdf specialities of SciPlore).

I really like your suggestion of "Compendium" - though I haven't yet seen any screenies of it, it certainly sounds like a possible alternative and probably something Puppy should have in its software arsenal - even if it isn't open source [Edit: Whups - released under LGPL by UK's Open University] and requires registration. I had a look through some of the reviews and, while a lot of it seems to be self-citing within a clique of technological epistemologists, it certainly seems worth a shot. Yes please - could you make your pet available to the general community, perhaps as a new thread in science/engineering or (better perhaps) Documents?

Many Thanks for all your help - I really appreciate it :)


PS To all - what I idly dream about is a FireFox add-on to enable dynamic mindmap-type manipulations of Zotero libraries... that would cut out a lot of "middle-apps"
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#12 Post by Puppyt »

Just a quick note:-
from http://www.sciplore.org/software/sciplo ... /en/#Linux:
Q: Does SciPlore MindMapping runs under Linux (Ubuntu 9.10)?
A: Some user managed to run the software. We can only encourage you to try (we will publish a special version for Linux soon). One user gave us a brief description how to run SciPlore MindMapping with Ubuntu 9.10:
It also runs fine on Ubuntu Linux 9.10- within the File Browser, I right-clicked on lib/freemind.jar and selected "Open with OpenJDK Java 6 Runtime".
OK so I installed jre-1.3.0.22.pet in dejan555's recent dpup485 puplet and we are talking chalk and cheese regarding the Ubuntu solution (AFAIK), but on reopening SciPlore 15, I now get a new error message when attempting to open PDFs (default to ePDFViewer).
I don't get encryption warnings, just "Error Loading File. Failed to open the PDF file. (mtPaint default gives the same error as before when trying to open a JPG from within SciPlore.)
I think I'm getting a liiiiiittle bit closer to working this out...
But if you are reading this and know the answer, don't just sit there chuckling to yourselves, please :oops: - Hook in and give me a clue!
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#13 Post by Puppyt »

Hmmm if I were a betting man, I'd say that /usr/share/sciplore-15/plugins/svg/pdf-transcoder.jar was partly to blame. Anyone is more than welcome to second the motion and suggest a solution...

[EDIT: Orighty - can't get my jar files 'clickable' (e.g., see http://murga-linux.com/puppy/viewtopic. ... 0333#30333) despite following the 'Set run action' from within ROX, plus launch script in usr/sbin. In response to "# java -jar pdf-transcoder.jar" run from terminal in the directory listed above, I get a "Failed to load Main-Class manifest attribute from pdf-transcoder.jar" message. Two sides to the same coin, I reckon, but I still could be swinging from the wrong branch in terms of solving PDF access within SciPlore...

NOOBSFLASH: Ok after trawling behind the scenes in the SciPlore directory listed at the top of this post I found that some .jar files were clickable (e.g., Freemind (SciPlore), JabRef2.6, others did nothing (and don't click on the SimplyHTML.jar file - that gives you the flash screen that never dies - across all desktops)). Then I hunted through the SciPloreMindMapping.sh to pick out the possibility that I needed OpenJDK-6-JRE. Downloading now and installing all dependencies, about 80Megs total, from the Debian repositories. Fingers crossed... ]

EDIT: :cry:

EDIT EDIT: http://murga-linux.com/puppy/viewtopic. ... 293#494293 Ariel posted this solution to FreeMind 2 months ago - I'm pinning my hopes that it will also work for it's bigger brother, SciPlore. :idea:

EDIT 2 DAYS LATER: Ok Ariel's FreeMind pets and recipe works also in Dpup485, but a re-installed SciPlore (removed first before the FreeMind dependencies were installed, just to be sure) wasn't successful and I got the same responses as posted earlier for images and pdfs. I'm still suspicious of pdf-transcoder.jar but don't have any idea about correcting this issue. I wonder whether the central hassle is related to how Puppy organises its java, and is being pointed to the wrong place i.e., where Debian etc might structure it in under "/usr/java/j2re1.4.2" whatever. Perhaps if the java pet(s) were removed and java reinstalled from the Debian repositories the problem might "go away" for a noob like myself.
No matter - I also tried to run the SciPlore exe under Wine in the same system and couldn't find a way to convince the install that I actually had the required version of java available. Again, it seems that perhaps it was looking in the wrong place for it. Giving up for now, sorry.
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#14 Post by Puppyt »

Cheers All -
revisiting this problem again briefly. I've just tested my previously-described hunch against some recent Puppy builds and ttuuxx's 2.14 remaster project. No joy still on any Puppy5 build with any attempted java recipe, as SciPlore's file linkageing (?) still opens text/doc files seamlessly with AbiWord - but incompletely opens PDF and JPGs with the same results described earlier. ttuuxx's rebuilt-from-scratch 2.14(TOP8) puppy has different behaviour: the docs open fine with his AbiWord, but FireFox is called to open ALL other file types I've placed in a SciPlore mind-map. Therefore it seems apparent (to me, a non-programmer) that as it is installed, SciPlore points its file attributes to incorrect applications/locations in the Puppy file structure.
Barked if I know how to identify and correct this wayward application-calling issue, but it would be well worth solving in the Puppy kennels as the SciPlore team has just been awarded 100 thousand Euros to further their project - so many see value in this application. And, there have already been major improvements since the SciPlore 15beta pet was submitted.

Apologies to any programmer who might be offended by my mixing incorrect terminologies in my update. Please don't let that put you off. Any suggestions in solving this probably simple problem would be most welcome :)
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#15 Post by ariel »

hi there,

I've got a hack that may help you out. have a look here

do you think I could claim my share of the 100.000? :lol:

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#16 Post by Puppyt »

Ariel!

You little beauty. I saw Marcello post on your FreeMind thread earlier, and will be trying your work-around in the morning (just turned pumpkin-hour here in East Oz). I've already given the Docear team a 'heads up' on this issue, and I'm sure that they've read the FreeMind and SciPlore threads in this forum but they are very busy with moving their base from FreeMind to FreePlane, so no direct remedies have appeared. Myself I've even tried symlinking in various directories - all dead-ended. I hadn't considered the xdg-open issue at all - here's hoping! I hope to attach a screenie of a PDF opened from within SciPlore, very soooooon....
Cheers!

PS I hope that they might toss a bit of their 100.000 your way - I'm guessing you're in Europe :)

UPDATE :
Ok I've followed your recipe outlined in the FreeMind thread, although I haven't installed your FreeMind pet. I've even installed the cgj-jre-4-4-4-3-lucid pet you had listed on that thread. Web-pages cast into the SciPlore mindmap open with default browser, FireFox (yay! Behaviour that I hadn't checked earlier), but I get no response when trying to open PDFs or JPG images, after openfile.sh pet is installed and the SciPlore Tools>Preferences>HTML >Default Browser command Other Os> ... changed to "openfile.sh {0}". Nada. No signs of activity, just stonewalling.
So something has changed in SciPlore's behaviour - and I'm thinking that your work-around is possibly the most likely solution, nonetheless. I'll try other puplets other than my early-lucid barebones base, and experiment with other java pets (currently using one of pemasu's, wondering if ttuuxx's pet might show something different). Hope to give more feedback later tonight. :)
Last edited by Puppyt on Thu 04 Aug 2011, 02:16, edited 1 time in total.
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#17 Post by Puppyt »

G'day again Ariel,

I've just run a frugal install of pemasu's Polarpup v 003 on my machine, installing ttuuxx's jre-6u26-1-i386, your cgj-jre-4-4-4-3-lucid, geoff's SciPlore15 pet, and then with reboots your openfile.sh and then even your FreeMind pet.
Strange - here the SciPlore flash title page halts while "Load maps..." but mindmaps can still be designed and saved. Didn't see that in my Lucid lite frugal environment - and not while using ttuuxx's java in dpup pupplets. My test mindmap, with PDF, html and jpgs on nodes returned the same behaviour as noted in my update in the previous post. Then tested Freemind, first without the change to the xdg-open default:

Code: Select all

sh-4.1# freemind
Checking Java Version...
java.io.FileNotFoundException: /root/.freemind/auto.properties (No such file or directory)
	at java.io.FileInputStream.open(Native Method)
	at java.io.FileInputStream.<init>(FileInputStream.java:120)
	at freemind.main.FreeMindStarter.readUsersPreferences(FreeMindStarter.java:136)
	at freemind.main.FreeMindStarter.main(FreeMindStarter.java:56)
Panic! Error while loading default properties.
Jul 31, 2011 9:45:09 PM freemind.main.FreeMindCommon$FreemindResourceBundle handleGetObject
SEVERE: Warning - resource string not found:OptionPanel.kr
And after changing to openfile.sh and restarting Freemind:

Code: Select all

sh-4.1# freemind
Checking Java Version...
Jul 31, 2011 9:49:04 PM freemind.main.FreeMindCommon$FreemindResourceBundle handleGetObject
SEVERE: Warning - resource string not found:OptionPanel.kr
sh-4.1# 
...so, I'm afraid I'm still completely in the dark about this issue. In ttuuxx's TOP8 214X I reported last week a different response where the default browser was called to (unsuccessfully) open pdfs and images. Wonder if your openfile.sh pet would work there?

Thanks for your help,
Puppyt
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#18 Post by ariel »

Puppyt wrote: I get no response when trying to open PDFs or JPG images, after openfile.sh pet is installed and the SciPlore Tools>Preferences>HTML >Default Browser command Other Os> ... changed to "openfile.sh {0}". Nada. No signs of activity, just stonewalling.
of course not. you are supposed to modify the script to suit your install :!:
for example add this line to the script to open a jpg file:

Code: Select all

elif [ "$ext" == jpg ] || [ "$ext" == JPG ] ; then viewnior "$@"
another catch is that you need a proper application that can open files with a command line. for pdfs you can use evince, for images viewnior, for htmls firefox, and so on...

i've just scribbled a fast and dirty script that needs your cooperation :)

for each kind of file check if there's the corresponding code to open it. if the script doesn't work add the necessary code or change it in /usr/bin/openfile.sh with a text editor. it should be a peace of cake even for bash illitarates.

if you wonder where to find evince you can GoNgetIT :wink:

Puppyt
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#19 Post by Puppyt »

:lol:
...bash illiterates, and ME! "None so blind...", as they say.
Brilliant, Ariel - I reckon I will have it going very shortly, later today. Thankyou VERY much for filling in that last piece of the puzzle for me! SciPlore/ Docear provides a MASSIVE tool to assist research and research writing, and although (I hope) their next round of updates are planned to include Preferences for the user to select and change their preferred apps for various file integration - removing this problem in future (I'm guessing) - it's been a bugger to have SciPlore only working, for me, in XP rather than Puppy.

3 Cheers for you, Ariel! :!: :!: :!:


PS I think I've tried eVince from a pet somewheres from the forum - one of my earlier dead-ends in trying to awaken SciPlore in Puppy... thanks for the link nonetheless - good backup avenue if things don't go 'ping' in the right way...
Last edited by Puppyt on Thu 04 Aug 2011, 02:24, edited 1 time in total.
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ariel
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#20 Post by ariel »

it's a fine pleasure to help get rid of the Redmond virusware :D


ps
i meant bash, the unix shell

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