I had a look at what happened to AceDB and it seems like it is now hosted on
https://github.com/ncbi/AceView/blob/master/w9/dotter.c
at least the dotter application that is. I find that tool of high (and
underrated)
educational and practical value and would not want to miss that.
I will not get
Hi Andreas,
I am afraid I cannot put the extra effort into those packages and, admittedly,
the NCBI software suite is just a bit intimidating, too. Please remove those
packages from testing and if nobody shows any interest in the required updates
then eventually those packages should also be re
On 30.06.22 11:51, Andreas Tille wrote:
I'd like to point out to this serious bug. Steffen, would you mind
koordinating (not doing alone) an upgrade of the qiime infrastructure to
make sure everything will go smoothly?
I added "to be updated" tags to all the qiime2 packages on
https://docs.g
The problem is with the tiff library. On
https://github.com/LinuxCNC/linuxcnc/pull/1700 it is explained how to
install an earlier version from snapshot.debian.org
To trigger the problem independently from linuxcnc, try
$ wish
% package require Img
The same error is triggered from within Tcl/Tk. LinuxCNC I do not think
to be to blame.
$ wish
% package require Img
couldn't load file
"/usr/lib/tcltk/x86_64-linux-gnu/Img1.4.13/libtifftcl4.1.0.so":
/usr/lib/tcltk/x86_64-linux-gnu/Img1.4.13/libtifftcl4.1
.0.so: undefined symbol: _TIFFsetString,
On 14.11.21 08:47, Andreas Tille wrote:
Control: blocked -1 by 995252
Hi Steffen
ERROR: dependencies ‘DRIMSeq’, ‘tximeta’ are not available for package
‘IsoformSwitchAnalyzeR’
r-bioc-tximeta is in Debian and just needs to be mentioned in
Build-Depends. However, Git seems not to be up to da
On 21.10.21 20:21, Étienne Mollier wrote:
Hi Andreas,
Andreas Tille, on 2021-10-21:
In file included from addtargets2.cpp:3:
myutils.h:176:1: error: reference to 'byte' is ambiguous
Since C++ 2017, the std::byte type is defined:
176 | byte *ReadAllStdioFile(FILE *f, off_t &FileSize);
Would a regular backport be the way to go?
Thank you, Logan.
I just fixed that and uploaded. Nothing new from upstream.
Steffen
https://github.com/samtools/htslib/issues/1098
http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics/src/commit/a2a200402b91a352dbdede01eec85accb892b8e1/htslib-add-cram_to_bam.patch
That patch just makes the cram_to_bam routine visible and should be
adopted without danger.
Steffen
A new version 5.7.3 is out, so I have addressed the "python" in the test
routines and wherever I encountered them.
Some tests still fail since files are written to the install folder
where they are not tested. Other comparisons now fail since there is a
linebreak in the help output where there wa
I am too busy to chase this all up, I am afraid.
On 07.12.19 09:04, Andreas Tille wrote:
Hi,
I just removed mgltools-pmv from debian-med metapackages to prepare its
removal. I realised that autodocktools depends mgltools-pmv so this has
to go as well. Since there is no sign that this 2.5 year
Hello,
On 08.11.19 23:14, Andreas Tille wrote:
On Fri, Nov 08, 2019 at 06:00:08PM +0100, Michael Crusoe wrote:
I got farther, but now the "dashboard" module won't load (no traceback).
The tests still fail spectacularly.
This is very old and non-free code. I suggest that all mglools* and
autodo
Hi Andreas,
thank you for the report. A "once worked" patch is part of
https://github.com/BOINC/boinc/pull/3259. No exact idea what this is
waiting for but I remain confident that it will eventually be accepted.
Cheers,
Steffen
Hi Adrian,
On 08.01.19 13:00, Adrian Bunk wrote:
Control: tags 913369 + patch
Control: tags 913369 + pending
I've prepared an NMU for pluto-jpl-eph (versioned as 0.0~git20180228-1.1) and
uploaded it to DELAYED/15. Please feel free to tell me if I should cancel it.
Thank you for your interest
Heya, I have replied, at least I had typed it :o/
So, yes, I had chosen that version of ffsort_index to get hhsuite to
compile. I have no idea if there are other reverse dependencies on
ffindex, my priority is on hhsuite.
Cheers,
Steffen
On 04.01.19 18:17, Michael Crusoe wrote:
I think 0.9.
Hi Andreas,
the reverse dependency HH-suite failed to compile with the ffindex
version Debian shipped.
I have no feelings about it. It should just work :) The HH-suite is
about structure prediction from sequence homology, which I found we
should continue to offer in our distribution
https:
Dear Aurelien,
The package compiles just fine with the later gcc version. But - and
this is a big but - about 10 to 25 percent of results produced with the
newer versions give slightly different results, i.e. different enough
that the difference between the g++ versions is bigger than the
dif
Hello,
I just introduced g++-5 as a build dependency to
https://packages.qa.debian.org/b/boinc-app-eah-brp.html because of small
- but very present - runtime differences. It had helped me a lot to have
g++-5 in unstable so I could just go and test. You certainly have
reasons to remove it, but
Well spotted, many thanks! If it is easy for you then I happily see you
uploading your fixed package to the distribution.
Steffen
Hi,
well done!
On 11/11/2016 13:06, Andreas Tille wrote:
> Hi Danny,
>
> thanks again for your help.
>
> On Fri, Nov 11, 2016 at 12:36:49PM +0100, Danny Edel wrote:
>> Control: block 784451 by 832420
>>
>> that is fine with me. I'll keep the bugs in CC too.
> :-)
>
>>> We somehow should targe
Go ahead. This pkg-escience was that Taverna collective effort.
Thanks
Steffen
On 20/06/16 15:38, Olivier Sallou wrote:
> I made a quick fix to switch to compat 9 and fix Java version to current
> jdk in sid.
>
> However, i cannot push to pkg-escience / bytecode (permission denied).
>
> It woul
Hi Andreas,
On 20/06/16 12:21, Andreas Tille wrote:
> Hi,
>
> the RC bug #817385 affects several Debian Med packages. IMHO it would
> be best if the package would be moved to either Debian Med or Debian
> Jave Git. The package is currently unmaintained (Steffen, please
> correct me if I'm wrong)
> I would highly appreciate if you can either allow me to push this as an NMU
> or
> just build+upload yourself.
Oh, please feel free to NMU - every piece of help is much appreciated.
Best,
Steffen
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> On Friday 05 June 2015 16:33:45 Lisandro Damián Nicanor Pérez Meyer wrote:
> > Mm, no, I'm afraid ball keeps FTBFS due to the same error:
> >
> > Linking CXX executable ../../../bin/BALLView
> > /usr/bin/ld: CMakeFiles/BALLView.dir/main.o: undefined reference to symbol
> > 'XInitThreads'
> > //u
Hello,
>Von: "Dominique Belhachemi"
>I agree that the 2.4 branch is completely outdated. We should switch to a
>newer branch.
>The 2.5 and 4.1 branches are not suitable for Debian due to licensing issues.
>But the 4.2 branch is licensed under the same license as the 2.4 branch, so I
>suggest
Thank you for your report. I just fail to understand
it, still. I just checked the source code and the arch
already comes from dpkg-architecture. The latest
with #711843 this should all be an issue of the past.
I to do not see why it works on amd64 but not for e.g. i386.
I need a mental reset, wi
Hello,
> In Debian, we are in the process of switching the default MPI
> implementation from version 1.4 to 1.6.
>
> Every architectures are fine beside ia64. Any program based on OpenMPI
> 1.6.5 is freezing.
>
> With a basic test case:
> MPI_Init(NULL, NULL);
> MPI_Finalize();
>
> mpirun -
> Gesendet: Dienstag, 27. August 2013 um 00:47 Uhr
> Von: "Emmanuel Bourg"
> An: 687...@bugs.debian.org, 687694-submit...@bugs.debian.org
> Betreff: Bug#687694: bouncycastle: 1.44 and 1.46 are not binary compatible
>
> Quick update on the remaining packages affected by the transition:
>
> jenki
Hello,
it is admittedly all a bit tedious because of conflicts with the regular Wine
package. But at least now (Jan 2013) it is
installable. And it works. Also coming from the win 1.4 package.
Steffen
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- Ursprüngliche Nachricht -
Von: Julien Cristau
Gesendet: 29.12.12 18:46 Uhr
An: Charles Plessy, 694...@bugs.debian.org
Betreff: [Debian-med-packaging] Bug#694908: Contains non-free data
On Sun, Dec 2, 2012 at 09:39:14 +0900, Charles Plessy wrote: > Package: emboss
> Version: 6.4.0-4 > S
Hi Andreas,
> any reason not to upload a fixed package incorporating the suggested
> patch?
Upstream did not react, yet. I was hoping for a quick adoption by upstream and
then a patch-free upload of that package. Need to ask again.
Cheers,
Steffen
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Hello,
On 10/17/2012 04:16 PM, Andreas Tille wrote:
> I admit that an empty package is not nice but from my perspective this
> bug does not qualify as severity "grave". I'm tempted to set this to
> "normal" - specifically in freeze time this severity might add noise
> we do not really need.
>
> W
Hello,
> Andreas Tille writes:
> > You are mixing up GPL and DFSG. GPL says that the source code needs to
> > be provided at least at request (and it in this case it is pretty easy
> > to obtain the source code).
>
> "The general rule is, if you distribute binaries, you must distribute
> the co
Hello,
Original-Nachricht
> Datum: Mon, 1 Oct 2012 08:49:55 +0200
> Von: Andreas Tille
> An: Jonathan Nieder , 645...@bugs.debian.org
> Betreff: [Debian-med-packaging] Bug#645487: ensembl: includes GPL code
> without source
> Hi,
>
> On Sun, Sep 23, 2012 at 07:00:23PM
On 07/26/2012 06:24 PM, gregor herrmann wrote:
> On Sat, 12 May 2012 17:05:13 +0200, Steffen Möller wrote:
>
>> Peter, have many thanks. I see what I can do over the weekend.
> Seems you're having a long weekend :)
Did I truly write that in May? Strange. I think to have alrea
Two HD5770 over here, was configured for two monitors on single device, but
even the simples variant led to the crash .. and ruined a day. Am back to the
free driver until the situation gets back to normal.
Steffen
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Thank you, Samuel.
Upstream is aware of this problem and also knows about next month's freeze.
They will do what they can do.
Steffen
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Hello,
I have just added the patch to the git repository and am very happy for
Paul and Ilya having been so proactive on it all. We need a new
maintainer for the boinc-app-seti package. Particularly for the advent
of more and more performant mobile phones, many of which running with
Linux, we shou
Peter, have many thanks. I see what I can do over the weekend. SZ from
upstream has rewritten that code and I wanted to address the ztex realm of
packages over the next days, anyway.
Are you using the ZTEX hardware by any chance? I was hoping for some FPGA
community to form over time with Debi
Fixed upstream. Did not get around to it.
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> original
> maintainers just pushed a broken package to experimental and take this
> distribution as an excuse not to care any more.
No really. The current packaging exactly matches the official
build instructions for Ensembl. That is quite a strong point,
at least for me. Any deviation from that
Hello,
On 01/24/2012 09:36 PM, Jonathan Nieder wrote:
> reassign 636923 ensembl 63-1
> severity 636923 serious
> quit
>
> Hi,
>
> Luca Falavigna wrote:
>
>> As there's little the FTP Team can do at this point, I'm reassigning
>> this bug to libwww5.808-perl source package, pending a proper fix.
Hello,
the same machine that previously built the BALL packages now fails in
just the same way you are describing it. I cannot tell what it is.
Upstream is informed and will certainly fix this at some point.
Many thanks for spotting this
Steffen
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, Andreas Tille wrote:
> Hi Steffen,
>
> could you please answer the more important piece I'm repeating below?
>
> Thanks
>
>Andreas.
>
> On Wed, Nov 30, 2011 at 10:37:11AM +0100, Steffen Möller wrote:
>>> Regarding fixing the actual problem I wo
Hello Jonathan,
Thank you for spotting the omission.
On 11/30/2011 09:58 AM, Andreas Tille wrote:
> Hi,
>
> On Sun, Oct 16, 2011 at 09:49:25PM +0200, Andreas Tille wrote:
>> On Sun, Oct 16, 2011 at 03:51:18AM -0500, Jonathan Nieder wrote:
>>> Unfortunately no such file exists --- I guess it disap
Hello,
On 09/26/2011 06:01 PM, Christoph Egger wrote:
> Your package failed to build on the kfreebsd-* buildds:
>
> make[1]: Entering directory
> `/build/buildd-boinc_6.13.1+dfsg-2-kfreebsd-amd64-XCjgHd/boinc-6.13.1+dfsg'
> docbook2x-man debian/manpages/update-boinc-applinks.xml
>
>
This removed the advert phenotype for me.
Steffen
# update-alternatives --config liblapack.so.3gf
There are 2 choices for the alternative liblapack.so.3gf (providing
/usr/lib/liblapack.so.3gf).
SelectionPathPriority Status
-
I just checked again,
On 09/03/2011 07:23 PM, Jakub Wilk wrote:
> Package: python-cogent
> Version: 1.5.1-1
> Severity: serious
> Justification: Policy 3.5
>
> In a minimal chroot:
> | $ python -c 'import cogent'
> | Traceback (most recent call last):
> | File "", line 1, in
> | File "/usr/l
ooops,
On 09/03/2011 07:23 PM, Jakub Wilk wrote:
> | import numpy
> | ImportError: No module named numpy
many thanks. I thought I'd have already fixed that one.
Will do,
Steffen
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Please accept the packages for now. I will be in San Diego for two days
meeting them in October. We get this somehow fixed. Any change to the
license would need to go through their law departments again ... which
had happened before and can happen again ... but we should not allow
ourselves to be i
Tags: wontfix
Thanks
Hi Christoph,
I am aware of those failures. PowerPC is new, indeed, the kfreebsd are old.
Those worked when
I created local virtual images with qemu of those kfreebsds, builing like a
charm.
It just took me half a weekend. That is why there was a 6.12.27 or so version
of
Hi Lucas,
On 05/02/2011 02:54 PM, Lucas Nussbaum wrote:
>> cd . && CFLAGS="-g -O2 -g -O2 -Wall -I/usr/lib/emboss/include
>> -I/usr/lib/emboss/include/epcre -I/usr/lib/emboss/include/eplplot
>> -L/usr/lib/emboss/lib -R/usr/lib/emboss/lib" CXXFLAGS="-g -O2 -g -O2 -Wall"
>> CPPFLAGS="" LDFLAGS="
qtdmm will soon be kicked out of the archive with the loss of qt3 ...
have many thanks for your investigation, but, the day only has 24
hours
Steffen
On 05/02/2011 02:37 PM, Lucas Nussbaum wrote:
> Source: qtdmm
> Version: 0.8.13-3
> Severity: serious
> Tags: wheezy sid
> User: debian..
Hello,
I am despaired over an error that was previously seen for both amd64 and i386 kfreebsds, and now remains with the i386 flavour.
The issue was not reproducible on either platform, squeeze or unstable, when running it virtually under qemu:
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=6
Dear fans of mgltools@Debian/Ubuntu out there,
some few extra weeks down the road there will be another
upstream release. Andreas was already so kind to
perform an update at least on the svn, many thanks
for that, I personally am too busy for an interim
reaction to the glut removal.
So, the summ
Hello,
CC to io admins.
On 04/10/2011 11:36 AM, Steffen Möller wrote:
I installed squeeze yesterday for kfreebsd in qemu and (after a long long time)
can report that the package is just compiling
nicely. The problem is most likely not with BOINC but of course we should use
that opportunity
Hello,
I installed squeeze yesterday for kfreebsd in qemu and (after a long long time) can report that the package is just compiling
nicely. The problem is most likely not with BOINC but of course we should use that opportunity to locate the bug. I'll see now if
I can reproduce the problem my u
Thank you Cyril.
This is now the second package of mine that "hangs" with kfreebsd. Seems like I
should get a virtual image of that running here.
There is nothing obvious for me to fix.
Volunteers welcome. I need to give this a month's rest.
Steffen
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Hi KiBi,
thank you for pointing this out. I already observed this for 6.12.15. The
package builds on everything except the i386 variant of
kfreebsd. I presume this to be a platform-specific error of the autotools or so.
On 03/20/2011 02:13 AM, Cyril Brulebois wrote:
> Source: boinc
> Version: 6.
On 01/25/2011 09:46 AM, Andreas Tille wrote:
> Hi again,
>
> On Tue, Jan 25, 2011 at 05:00:27PM +0900, Charles Plessy wrote:
>>> while the bug would be fixed in unstable after a simple rebuild it
>>> concerns the Squeeze release. I prepared a fixed version of the package
>>> (see debdiff).
>>
>>
Hello,
> your package still doesn't build:
> | libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../lib -pthread -g
> -O2 -g -Wall -O2 -g -Wall -O2 -Wall -MT libboinc_graphics2_la-reduce_lib.lo
> -MD -MP -MF .deps/libboinc_graphics2_la-reduce_lib.Tpo -c reduce_lib.cpp -o
> libboinc_graphics
On 01/01/2011 01:35 PM, Adam D. Barratt wrote:
> On Fri, 2010-12-31 at 17:08 -0800, Josh Triplett wrote:
>> I don't know whether to report this bug against paml-doc or
>> ftp.debian.org.
>
> It's definitely a bug in paml. Arguably dak shouldn't allow the
> situation to occur in the archive, but t
On 12/31/2010 05:38 PM, Cyril Brulebois wrote:
> Source: boinc
> Version: 6.12.8+dfsg-1
> Severity: serious
> Justification: FTBFS
>
> Your package no longer builds:
> | /bin/sh: libtoolize: not found
>
> KiBi.
Thank you, KiBi. As a quick fix, please "sudo apt-get install libtool".
I'll have tha
Hello,
thank you all for caring for the mgltools,
but I think this is all too late and too uncertain
for us to proceed for squeeze. I already got this
confirmed by the release managers. We should now bet
on backports and I'll have autodocktools and mgltools-*
removed from squeeze. This shall
a) he
Hi Gregor, have many thanks! I'll upload later tonight.
Best,
Steffen
On 10/25/2010 12:25 AM, gregor herrmann wrote:
> On Mon, 27 Sep 2010 15:30:57 -0300, Nelson A. de Oliveira wrote:
>
Configuring the package with --enable-dummy works on powerpc (tested
on pescetti.debian.org).
>> On
It also needs the hibernate v 3.3 packages. Ping me if you want to try
again, I'll place them on an apt repository for you.
Best,
Steffen
On 09/24/2010 03:41 PM, gregor herrmann wrote:
> On Thu, 29 Jul 2010 13:35:35 +0900, Charles Plessy wrote:
>
>
>> no news. Given that Eucalyptus in Debian
Hello,
On 09/17/2010 05:12 PM, Miguel Landaeta wrote:
> On Sun, Aug 15, 2010 at 09:47:01AM +0200, Lucas Nussbaum wrote:
>
>> Source: eucalyptus
>> Version: 1.6.2-2
>> Severity: serious
>> Tags: squeeze sid
>> User: debian...@lists.debian.org
>> Usertags: qa-ftbfs-20100815 qa-ftbfs
>> Justificat
Hi Charles,
sounds good to me, too! The Java community has lots of such internal
libraries and your issues seem to be of the same nature. Have many
thanks for your efforts,
Steffen
On 09/13/2010 07:17 AM, Charles Plessy wrote:
> Dear all,
>
> the EMBOSS libraries sometimes break backwards compa
Hello,
this is somewhat mysterious to me. I presume that altivec is kind of found but
also not configured at the same time. Charles, I
recall you to be a PowerPC user, could you please test this
--- debian/rules(revision 5197)
+++ debian/rules(working copy)
@@ -3,8 +3,19 @@
inclu
On 08/17/2010 02:11 PM, Maciej Gałkiewicz wrote:
> Now it works! Thank you very much.
>
May I just ask what you have done? Was it a restart of the System or any
change of the configuration?
Thanks and regards
Steffen
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Just a hunch. Could you please reinstall the previous version of
libhibernate? This has been updated to 3.5.4.Final very recently and
while reading "hibernate" so often in your report below this just kind
of triggers me thinking that we might possibly first search there.
To get there, you'd
sudo a
On 08/16/2010 11:21 PM, Debian Bug Tracking System wrote:
> This is an automatic notification regarding your Bug report
> which was filed against the libhibernate3-java package:
>
> #593254: conflict with hybernate-entitiymanager-java 3.4.0 on .jar
libhibernate-entitymanager-java
It has not yet
Hello,
this license is more liberal than the GPL. Are you linking
against anything that is purely GPLed? Then we'd need to
do some thinking. I could imagine that you could even
relicense it as it also allows the "sublicensing", but this
is beyond my legal understanding. I hope we don't need
to cl
Hello,
thank you for this pointer. The mgltools packages are all due for an overhaul.
I'll address them all this week.
Have many thanks
Steffen
On 08/09/2010 09:21 PM, Jakub Wilk wrote:
> This is an FHS violation.
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severity 589815 normal
tags 589815 confirmed
thanks
Dominique, great job! I was not aware of the groovy.jar
in /usr/share/eucalyptus.
On 07/24/2010 08:41 PM, Dominique Belhachemi wrote:
> this temporary workaround might help.
>
> mv /usr/share/eucalyptus/groovy.jar /usr/share/eucalyptus/groovy.ja
Hello,
> Dear maintainer,
>
> I've prepared an NMU for mgltools-vision (versioned as
> 1.5.4.cvs.20090603-1.1) and
> uploaded it to DELAYED/3. Please feel free to tell me if I
> should delay it longer.
great! Thanks!
> Regards.
>
> PS some tests still fail (same number for Python 2.5 and Python
On 06/30/2010 09:27 AM, Ralf Treinen wrote:
> After the recent transition of phython-2.6 to testing, this makes
> mgltools-gle also uninstallable in testing.
>
Pjotr, can you please address this one and all the other mgltool-*
packages that are not autobuilt, too?
Many thanks
Steffen
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On 06/30/2010 09:05 AM, Piotr Ożarowski wrote:
> [Charles Plessy, 2010-06-30]
>
>> What makes you think that autodocktools works with python 2.6 if upstream
>> hardcoded it for 2.5. Have you tested the package before uploading?
>>
>> I understand that you may be disapointed that we have not answ
Hi Torsten,
> Datum: Sat, 19 Jun 2010 00:23:17 +0200
> Von: Torsten Werner
> Am 18.06.2010 21:42, schrieb "Steffen Möller":
> > this grub version needs to be removed immediately from unstable.
>
> just purge the grub2 related binary packages from your s
Hello,
this grub version needs to be removed immediately from unstable. It discourages
enormously the use of unstable to filter for testing.
The /boot/grub/stage/stage2 and stage1 files are existing on my system.
Maybe I was too happy with unstable for too long and have given my 64bit
res
Hello,
> your package FTBFS everywhere:
> | # Add here commands to clean up after the build process.
> | [ -r Makefile ] && /usr/bin/make distclean
> | make: *** [clean] Error 1
>
sorry, it should have been ! -r and ||
Thanks, I'll upload later tonight, please feel free to NMU should you be
usi
Hi Ralf,
this is a great service of yours.
On 05/17/2010 08:39 AM, Ralf Treinen wrote:
> this isn't solved yet for torque-doc which still clashes with
> gridengine-client:
>
> dpkg-deb: subprocess paste killed by signal (Broken pipe)
> Processing triggers for man-db ...
> Errors were encounter
Hello,
Teodor schrieb:
> On Tue, Oct 28, 2008 at 12:54 PM, Steffen Möller <[EMAIL PROTECTED]> wrote:
>
>> Charles Plessy schrieb:
>>
>>> Le Tue, Oct 28, 2008 at 09:32:42AM +0200, Teodor a écrit :
>>>
>>>> I still believe it
Charles Plessy schrieb:
> Le Tue, Oct 28, 2008 at 09:32:42AM +0200, Teodor a écrit :
>
>> I still believe it is best to rename 'plink' to 'puttylink' in
>> putty-tools binary package. Anyway, this should be fixed for squeeze
>> since in lenny there is no conflict (plink is not included in lenny)
Hello,
plink has just made it to the archive.
Teodor happened to have nicely explained my objections to rename plink.
Dear Colin, if you don't mind too much, or if you could be bribed with a
few beers, please be so kind to rename the plink binary package.
Many thanks and best regards,
Steffen
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