> I'm just undecided because slurm itself needs
a bit more than just install the client package and you have immediate
advantage without more administration.
if I may: maybe gnu parallel would be a good suggestion, as well?
On Thu, Nov 2, 2023 at 7:21 AM Andreas Tille wrote:
> Hi Tony,
>
> Am
Cool! May I please get an invitation?
Best Regards,
George Marselis
From: users on behalf of Ralph H Castain
Sent: Tuesday, March 5, 2019 5:12 PM
To: Open MPI Users
Subject: Re: [OMPI users] IRC/Discord?
Not IRC or discord, but we do make
Hey guys,
Sorry to bother you. I was wondering if there is an IRC or discord channel for
this mailing list.
(there is an IRC channel on Freenode under #openmpi but it's like 2 people in
it)
Thank you for your time
Best Regards,
George Mar
that also means there is a need for the maintainers of packages such as
galaxy or taverna to be notified and/or make sure when used in a pipeline
tophat throws a yuge error.
On Sat, Dec 16, 2017 at 8:00 PM, Fabian Klötzl
wrote:
> Hi,
>
> On 16.12.2017 15:40, geo...@marsel.is wrote:
> > There ar
on is better for you.
> As with regard to Martin, he should not use parallel for
^-- this is your brain on Perl.
Best Regards,
George
On Wed, Apr 15, 2015 at 11:27 PM, George Marselis wrote:
> Giuseppe, I was referring to both of you. My apologies I was not clear, I
> had my head stuck
do better with chunksize (I have 1 record at time
> in my example) but that's a secondary problem now. First I have the
> "lsb_launch(): Failed while waiting for tasks to finish." issue to solve.
>
> cheers,
>
> g
>
>
>
>
> On Wed, Apr 15, 2015 at 7:44 PM
-q smalljobs qfasta file2
...
bsub -J amoeba -q smalljobs qfasta file2000
On Wed, Apr 15, 2015 at 8:39 PM, George Marselis wrote:
> Hi. LSF/Openlava sysadmin in bioinformatics and parallel user here.
>
> I have seen this a couple more times: You are trying to use GNU parallel
> to sub
bmit all 2000 jobs in less
than a second, you can do it from a single node and you will not have to
deal with a grumpy sysadmin or grumpy colleagues who cannot use the
cluster. Just make sure you use the appropriate queue.
Let me know if you have any questions.
Best Regards,
George Marselis
not find anything
relevant.
May I please have a clue? What configuration parameter did I miss?
Best,
George Marselis, systems administrator
Building #1, Level 0, Office Area 0203-WS16
Visualisation Laboratory, KAUST
Land: +966-2-808-0634, Mobile: +966-56-321-7713, Skype: project2501a
>
> I am not sure I understand this at all. If your input is part of a
> name of a compressed file and the output is the uncompressed, I do not
> see a way for GNU Parallel to figure out how much space the
> uncompressed will take.
>
>
True. that is what i get for touching the keyboard before I ha
hey guys,
just finished reading the documentation for GNU parallel.
in the section titled "DIFFERENCES BETWEEN GNU Parallel AND ALTERNATIVES"
could you please mention (even honorary) the difference between GNU
parallel and dsh (dancer's shell ) / pdsh (parallel distributed shell) ?
thank you :)
hey guys.
i executed the above example from the manual in my bash shell.
i got back the following results:
[gmarselis@4jane ~]$ parallel echo {1} {2} {3} ::: 6 7 ::: 4 5 ::: 1 2 3
6 4 1
6 4 3
6 5 1
6 5 2
6 5 3
7 4 1
7 4 2
7 4 3
7 5 1
7 5 2
6 4 2
7 5 3
i would have guess that { 6, 4, 2 } would
Wow. Do they need sysadmins, as well?
On Fri, Dec 14, 2012 at 7:38 AM, Charles Plessy wrote:
> Hello everybody,
>
> As you may know I am working at RIKEN in Japan where I analyse the
> expression
> of genes and the mechanism of their regulation using molecular biology and
> bioinformatics. RIK
Wow. Do they need sysadmins, as well?
On Fri, Dec 14, 2012 at 7:38 AM, Charles Plessy wrote:
> Hello everybody,
>
> As you may know I am working at RIKEN in Japan where I analyse the
> expression
> of genes and the mechanism of their regulation using molecular biology and
> bioinformatics. RIK
Hey guys,
can you please make sure you bring large and xl LOPSA t-shirts around?
thank you!
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Sorry, I should have included the URL:
ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/
does that ring a bell?
On Fri, Aug 3, 2012 at 2:37 PM, Olivier Sallou wrote:
>
> Le 8/3/12 1:25 PM, George Marselis a écrit :
>
> Hey guys,
>
> I am confused: I am trying to find out to wh
Hey guys,
I am confused: I am trying to find out to which Debian package do the
NCBI Tools++ software map to; a bit of googling did not come up with
anything consistent. Any clues, please?
Thank you.
George Marselis
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"Debian; I'm just sayin'" http://www.youtube.com/watch?v=4bhrSqBgrHI
"'Support Contract' is a nice way of describing that our sysadmins are
not technically inclined" oh, wait, you said "nice" :D
PS: Wanted: Sysadmins and programmers with neck-beard and jeans to
re-shoot the original (cuz i got a
tl;dr : http://www.youtube.com/watch?v=8oz7dqy0Ft4
2012/3/12 Simos Xenitellis :
> Παρακολουθώ με ενδιαφέρον όσα λέγονται στη λίστα αυτή.
auto eleipe. na mhn yparxei kai cliff hanger.
> Ένα από τα στραβά που βλέπω είναι ότι η ανακοίνωση για το
> planet.gnome.gr έχει φύγει οφφ-τόπικ.
> Αν είναι μ
r this.
Thank you, again!
Best,
George Marselis
Non ex transverso sed deorsum
[1] does not involve arrows into the knee
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my processes will always love you!
On Thu, Feb 23, 2012 at 1:30 AM, Ole Tange wrote:
> GNU Parallel 20120222 ('Whitney') has been released. It is available
> for download at: http://ftp.gnu.org/gnu/parallel/
>
> New in this release:
>
> * --workdir . will use the current working dir. If the curre
bbam-dev be an acceptable solution till i finally
finish the autotools book and submit a patch to upsteam?
thank you,
george marselis
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On Tue, Nov 1, 2011 at 12:37 AM, John G. Heim wrote:
>> Did you, possibly together with a co-worker, actually try that route of
>> manually
>> repairing the Windows install? If yes, did it do any good?
>
> Yes, I just tried that and it did work. So at the moment, I have a working
> Win7/linux mach
. Please let me know what you need from me.
Thanks!
George Marselis, systems administrator
Building #2, Level 4, room 4327
Computational Bioscience Research Center, KAUST
Land: +966-2-808-2944, Mobile: +966-56-321-7713, Skype: project2501a
Yes, your java path is not set, because you are using an non-login shell.
Indeed, you should be talking to your sysadmins.
George Marselis, systems administrator
Building #2, Level 4, room 4327
Computational Bioscience Research Center, KAUST
Land: +966-2-808-2944, Mobile: +966-56-321-7713
ncbi-blast+ . am I mistaken?
On Sun, May 29, 2011 at 3:04 PM, Olivier Sallou wrote:
> Hi,
> are you talking of blast or blast+ ?
>
> Regarding features, I do not see what you mean by xalan feature, or uuid
> (sounds like java packages).
>
> Olivier
>
> - Mail or
since we are on the subject, i have been trying to compile ncbi-blast
on my own, for my own use. i would like to enable ever single one of
it's features; eg, UUIDs . or xalan. I cannot find any info on how to
activate UUIDs (it's not an option in ./configure --help) and I cannot
find the proper de
> I fixed some mistakes - you might like to read my commit logs.
just svn updated, will read them after work.
>> SNAP, repeatmasker, trf, augustus, mugsy, apollo, chado, eHive, ECHO,
>> ANNOVAR, CMap, GBrowse_syn, JBrowse, Trupal
>
> I wonder why you added trf if
>
> License: binary only (non-f
, GBrowse_syn, JBrowse, Trupal
Thank you very much.
On Fri, Apr 22, 2011 at 1:18 AM, Andreas Tille wrote:
> So this
>
> https://alioth.debian.org/users/project2501a-guest/
>
> seems to be a different George Marselis which controls the e-mail
> address geo...@marsel.is and is
15, 2011 at 08:26:48PM +0100, George Marselis a écrit :
>> http://www.yandell-lab.org/software/maker.html
>>
>> with how-to here: http://gmod.org/wiki/MAKER_Tutorial#Installation
>>
>> how are you guys doing? :D just came back from london. i have to say:
>> god bless
r" gbrowse is now packaged and available in
> Debian unstable.
>
> Kind regards
>
> Andreas.
>
> On Tue, Apr 19, 2011 at 01:45:48PM +0300, George Marselis wrote:
>> Hey guys,
>>
>> I am working on GMOD ( http://gmod.org/wiki/Main_Page ). As you can
>
Hey guys,
I am working on GMOD ( http://gmod.org/wiki/Main_Page ). As you can
see for yourselves, that page was not created with a technical guy in
mind. I need to make a summary of that page. I was wondering where I
should put it. Is the Debian Wiki an acceptable solution?
Thank you,
George
i can definitely diff the sources. let me see what i can get.
On Sat, Apr 16, 2011 at 10:19 PM, Andreas Tille wrote:
> On Fri, Apr 15, 2011 at 11:34:35PM +0100, George Marselis wrote:
>> Hey guys,
>>
>> Apparently, repeat masker comes with its own version of Blast:
>>
wer any of your questions about this.
>
> Kind regards
>
> Andreas.
>
> On Sat, Apr 16, 2011 at 12:54:13AM +0100, George Marselis wrote:
>> http://exon.biology.gatech.edu/ for general description
>>
>> http://exon.biology.gatech.edu/license_download.cgi to downloa
On Sat, Apr 16, 2011 at 5:59 AM, Yaroslav Halchenko
wrote:
> Hi George,
Hello!
> To upload into Debian non-free, someone would
> need to be really interested in having it there. Otherwise, if it
> is not even satisfying requirements for Debian non-free, I guess there
> is nothing to discuss unf
http://exon.biology.gatech.edu/ for general description
http://exon.biology.gatech.edu/license_download.cgi to download the binaries
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Hey guys,
Apparently, repeat masker comes with its own version of Blast:
http://www.repeatmasker.org/RMBlast.html
they say that "RMBlast is a RepeatMasker compatible version of the
standard NCBI BLAST suite. The primary difference between this
distribution and the NCBI distribution is the additio
http://www.repeatmasker.org/
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It is off the page of Dr ian Korf at UC Davis Genome Center.
http://homepage.mac.com/iankorf/ He is one of the Authors of the
O'Reilly "BLAST" book
http://homepage.mac.com/iankorf/snap-2010-07-28.tar.gz
the program is under GPL 2
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Hey guys,
As you all know, a lot of bioinformatics programs come in nonfree
packaging. Newbler comes easily to mind.
What is the policy for including software in debian-med? I mean, free
software uber alles, yes, but some people will just not release the
software under the gpl. what then? For exa
> Fine. I hope you as well. You did not answered my question whether
> you need help with arachne and I have not noticed any commit.
>
> Kind regards
>
My apologies, I was in vacation and I was not reading my emails. No, I
have not done anything with arachne. I came back last night and I just
wo
http://www.yandell-lab.org/software/maker.html
with how-to here: http://gmod.org/wiki/MAKER_Tutorial#Installation
how are you guys doing? :D just came back from london. i have to say:
god bless the Queen for allowing her subjects to create such a diverse
line of beers!
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Oh. right :) yes, you are correct. never committed anything to git.
On Tue, Apr 5, 2011 at 9:53 PM, Andreas Tille wrote:
> On Tue, Apr 05, 2011 at 09:47:39PM +0300, George Marselis wrote:
>> i thought i already did have permissions, from my attempt with Mira.
>> Let me check a
i thought i already did have permissions, from my attempt with Mira.
Let me check again.
On Tue, Apr 5, 2011 at 6:29 PM, Andreas Tille wrote:
> On Tue, Apr 05, 2011 at 05:30:42PM +0300, George Marselis wrote:
>> http://www.broadinstitute.org/crd/wiki/index.php/Arachne#Download_Arachne
Um beginner, reporting in!
On Tue, Apr 5, 2011 at 6:23 PM, Andreas Tille wrote:
> On Tue, Apr 05, 2011 at 03:24:28PM +0100, Maximilian Haussler wrote:
>> Isn't the real upstream of meta-velvet here:
>> https://github.com/hacchy/MetaVelvet
>>
>> Based on:
>> http://metavelvet.dna.bio.keio.ac.jp/in
http://www.broadinstitute.org/crd/wiki/index.php/Arachne#Download_Arachne
can you list this program, as wel, please?
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hey guys,
i am trying to compile amos from source. it apparently requires qt3.
will the latest version of qt will do? anybody got a clue? or rather,
i will report myself as well, as soon as i finish compiling
oy!
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with a subjec
requirements? Stuff like that... If I could get a mentor
to help me over the initial hump, I would def be of use around here
(but no learning Java, please).
All the Best,
George Marselis, systems administrator
Building #2, Level 4, room 4327
Computational Bioscience Research Center, KAUST
Land:
I will ask about ssaha2 and i will follow with a letter similar to the
soapdenovo one. as i said we got sanger and ebi people here.
while we are suggesting packages, have you guys seen this tool?
http://sourceforge.net/apps/mediawiki/denovoassembler/index.php?title=Main_Page
NGE sequencer using
> I do not really get it. I find most of those tools already in
> Debian. bwa, mummer,samtools,velvet are in ... not sure
> about the state of the others.
i am inexperienced in the field of bioinformatics. i thought i would
gain more experience, by first making a list of all the tools used in
the
I apologize for the delayed reply, but I just had a flood in my
apartment. I love living in KAUST <3
Right now, the apartment is flooded with water from the fire
extinguish valve and there is no electricity. it will take me an hour
to go to the kaust coffee shop and set up my laptop from there
>
touch with whatever ideas or needs are popping
> up on your side.
>
> Best regards,
>
> Steffen
>
> [1] http://www.eaglegenomics.com/2011/01/symposium2011/
>
> On 03/30/2011 04:58 PM, George Marselis wrote:
>> great job, man. this will def minimize my headaches ...
&g
great job, man. this will def minimize my headaches ...
On Wed, Mar 16, 2011 at 1:37 PM, Steffen Möller wrote:
> Dear all,
>
> we can be very happy to now have Ensembl in our distribution. It is in
> experimental since it depends on other packages that are still in
> experimental. It is in non-f
hey guys,
to make up for some past sins with mira, I thought i would check with
the soapdenovo site.
it is now under the GPLv3 http://soap.genomics.org.cn/soapdenovo.html
Well done to the soapdenovo team and andreas for writing that email.
Best Regards,
George.
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yeah, that was my doing, but i sorta abandoned the project, because I
could not create a perfect package, and i shied away from asking on
the list in fear of sounding like a fool.
if i can help with anything, let me know
Best Regards,
George
On Wed, Mar 9, 2011 at 3:01 PM, Steffen Möller wrote
Hey guys,
Is there an irc channel for galaxy? I googled for "galaxy irc" but all I
see in the first fifty results are entries for the samsung galaxy (which
is an excellent phone ;)
Best Regards,
----
George Marselis, systems administrator
Building #2, Level 4, room 4327
Computational
George Marselis, systems administrator
Building #2, Level 4, room 4327
Computational Bioscience Research Center, KAUST
Land: +966-2-808-2944, Mobile: +966-56-321-7714, Skype: project2501a
___
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And before our release
>> of the code, it would be our honor to keep using your's resource to compile
>> the latest version of SOAPdenovo if it's acceptable
>>
>>
>> Best!
>>
>> RuiBang Luo
>> BGI-Shenzhen
>>
>>
>>
>>
hey guys, I have to hand it to the soap denovo people. Ruibang Luo
actually spent some of his precious time
to help me out at KAUST, where we have a pretty peculiar setup: Power7
series with 512GB of RAm and ugh, RHEL 5.4. It would be godsend if
they would publish the binary on their site or publi
a repo up, which can build a package from source.
the question now is how do i make it available for more machines than
amd64
that's for now, i will bug you all later :)
Regards,
George Marselis
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The following commit has been merged in the master branch:
commit ee7a7bd72d5a87975c45b4bb8461d31d3f5b19d9
Author: George Marselis
Date: Mon Sep 6 16:13:15 2010 +0300
added todo list
diff --git a/TODO b/TODO
new file mode 100644
index 000..641f981
--- /dev/null
+++ b/TODO
@@ -0,0 +1,5
The annotated tag, upstream/3.0.5 has been created
at 45e0aa94dfef9ed3167261c7b8877042054d9ce1 (tag)
tagging 4a4f78cb20ff29bc3c1ea4ec998564ebf53ca6f2 (commit)
tagged by George Marselis
on Fri Sep 3 18:18:58 2010 +0300
- Shortlog
The branch, upstream has been created
at 4a4f78cb20ff29bc3c1ea4ec998564ebf53ca6f2 (commit)
- Shortlog
---
--
MIRA Sequence and Shotgun DNA Assembler
The branch, master has been created
at 2da329211e11747c6a84228c905ead3005203c64 (commit)
- Shortlog
commit 2da329211e11747c6a84228c905ead3005203c64
Author: George Marselis
Date: Sat Sep 4 02:29:07 2010 +0300
initialized
tatement with your
installation
InterPro - Integrated Resource Of Protein Domains And
Functional Sites
Copyright (C) 2001 The InterPro Consortium.
so, this is definitely possible, but the framework needs cleaning up
and disentanglement.
> Best,
>
> Steffen
>
Regards from Saudi Ara
> Hi George,
>
> please enjoy Git! I have added you to the debian-med Alioth project, so you
> can
> add repositories in ssh://git.debian.org/git/debian-med. I am sorry that I
> have
> not managed to add instruction in the Debian Med policy yet. But you can find
> a lot of hints on the Debian wik
ions :)
thank you :)
Regards,
George Marselis
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hai hai! i am talking with Bastien, trying to convince him to release
the source out of CVS, else I will make vendor branches out of his
releases.
have some sake for me, please :)
thank you.
> Dear George,
>
> There is a preliminary package in our subversion repository:
>
> http://svn.debian.or
superseding #435915, which has not been acted upon ever since 2007.
I work full-time in bioinformatics, in KAUST, in saudi arabia, and I
plan to package as much as bioinformatics programs as possible.
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Package: wnpp
Severity: wishlist
Owner: George Marselis
* Package name: mira
Version : 3.0.5
Upstream Author : Bastien Chevreux
* URL :
http://sourceforge.net/apps/mediawiki/mira-assembler/index.php?title=Main_Pa
ge
* License : GPL
Programming Lang: C
superseding #435915, which has not been acted upon ever since 2007.
I work full-time in bioinformatics, in KAUST, in saudi arabia, and I
plan to package as much as bioinformatics programs as possible.
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Package: wnpp
Severity: wishlist
Owner: George Marselis
* Package name: mira
Version : 3.0.5
Upstream Author : Bastien Chevreux
* URL :
http://sourceforge.net/apps/mediawiki/mira-assembler/index.php?title=Main_Pa
ge
* License : GPL
Programming Lang: C
Package: wnpp
Severity: wishlist
Owner: George Marselis
* Package name: mira
Version : 3.0.5
Upstream Author : Bastien Chevreux
* URL :
http://sourceforge.net/apps/mediawiki/mira-assembler/index.php?title=Main_Pa
ge
* License : GPL
Programming Lang: C
nip]
>
> Bug report should describe situation objectively. This helps everyone.
I will do better next time. thank you for an excellent example of what a
description should have been.
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Building #2, 4th Floor, Room 4327
Computational Bioscience
-- System Information:
Debian Release: squeeze/sid
APT prefers testing
APT policy: (500, 'testing')
Architecture: amd64 (x86_64)
Kernel: Linux 2.6.32-5-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
--
Georg
Package: maint-guide
Version: 1.22-svn, 2010-08-18 03:39:54 UTC
Severity: minor
Tags: squeeze
there is an empty page on the current version of debian maint-guide,
english. this probably due to the
template formating, but i don't know how to fix it.
let's save a tree, guys :)
-- System Informa
Package: nfs-common
Line 12 reads
# For more information, see rpc.statd(8) or
http://wiki.debian.org/?SecuringNFS
It should read
# For more information, see rpc.statd(8) or
http://wiki.debian.org/SecuringNFS
Question mark is extra
--
George Marselis : systems administrator
Building #2, 4th
Package: nfs-common
Line 12 reads
# For more information, see rpc.statd(8) or
http://wiki.debian.org/?SecuringNFS
It should read
# For more information, see rpc.statd(8) or
http://wiki.debian.org/SecuringNFS
Question mark is extra
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George Marselis : systems administrator
Building #2, 4th
James Youngman wrote:
It's not such a great idea to do that. Far better to chop that up
into at least 1000 subdirectories. But take care not to use more than
about 32,000 subdirectories, as some Linux filesystems either don't
allow it (ext3) or some operations become less efficient at that poi
ittle python script together, but i can't
help thinking that this is a feature that will be needed in the future,
with bigger filesystems.
thank you for your time and again, thanks for making my life as a geek
enjoyable :D
George Marselis,
a geek from NJ
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May I recommend some Terry Pratchett, ie "Going Postal", or if you are
politically active, Mummia Abu-Jamal's "From Death Row", then, which is also
available on podcast from the itunes store. Or Umberto Eco's "Pantolino". I
assume you'll be going to the Data Center by train?
Have a safe trip.
And that's what you get for not RTFemail... you can enable
Remote desktop from well, remote.
http://www.intelliadmin.com/blog/2006/06/remotely-enable-remote-desktop.html
There we go. Sorry for being an idiot in my previous email
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he admin account. And you won't even have to install any kind of
vnc or terminal licenses, provided you only need only one or two admins. Plus
you get the benefit of Active Directory integration.
All Hell From The Scary Devil Monastery / Non ex transverso sed deorsum
Ge
What's the error message? Did you configure RealVNC as a service or user-run?
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Et Afrikalis Gladium Est
> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
> Behalf Of frankske D
> Sent: Thursday, August 30, 2007 11:01 AM
> To: vnc-list@realvnc.com
> Subject: C
Fishing in the dark here: What could the possible cause of a "Digest mismatch"
error be?
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Is there a -generatekeys command-line option? I've been trying to generate the
RSA key from the prompt.
Thanks
George Marselis
System Programmer
Achaiki Cooperative Bank
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>I would imagine you're doing this to build some sort of FAQ or
>document? :-)
>
> Casey West
yes, i am. the CGI books/FAQs i've read, don't deal with bugs very in
depth. they just mention the 500 internal error, chmod 700|755
Hey guys,
i'm trying to compile a top ten of why your forms break, i.e. you try to
press a submit button but it doesn't work.
any ideas?
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