Re: Latest blog post

2011-08-22 Thread Nelson A. de Oliveira
Hi! On Mon, Aug 22, 2011 at 12:34 PM, Steffen Möller wrote: > For the future, is there a way to have some bits not forwarded? > Or to have them only selectively forwarded? Well, the mailing > list, probably. You can tag the posts and have a RSS (for that specific tag) that will be published in P

sofa-framework failing to build

2011-08-18 Thread Nelson A. de Oliveira
Hi! After updating sofa-framework (both the build-deps for the new libqwt-dev and an include path) I can't pass this: http://people.debian.org/~naoliv/misc/sofa-framework_1.0~beta4-6_i386.build.txt Any ideas/suggestion/patches? :-) Latest debian/ dir is in our SVN. Thank you! Best regards, Nel

Re: debian-med svn checkout

2011-08-11 Thread Nelson A. de Oliveira
Hi! On Thu, Aug 11, 2011 at 1:25 PM, Dominique Belhachemi wrote: > It still doesn't work for me. All I get is the following error message: Can you ssh directly to the host? Are you using VerifyHostKeyDNS in your ~/.ssh/config for Debian hosts? "ssh -v svn.debian.org" can give us more info (you

Re: debian-med svn checkout

2011-08-11 Thread Nelson A. de Oliveira
Hi Dominique! On Thu, Aug 11, 2011 at 1:04 PM, Dominique Belhachemi wrote: > Does the following description work for anyone since the changes on alioth? For SVN it works: svn co svn+ssh://svn.debian.org/svn/debian-med/trunk/ For git: git clone git+ssh://git.debian.org/git/debian-med/package.g

Re: "Could not perform immediate configuration" with debian-med

2011-08-05 Thread Nelson A. de Oliveira
Hi! On Fri, Aug 5, 2011 at 1:24 PM, Scott Cain wrote: >  E: Internal Error, Could not perform immediate configuration (2) on > perl-modules It seems to be http://bugs.debian.org/548848, http://bugs.debian.org/548860 and others Best regards, Nelson -- To UNSUBSCRIBE, email to debian-med-requ..

Re: Blog about Debian Med BOF

2011-08-03 Thread Nelson A. de Oliveira
On Wed, Aug 3, 2011 at 8:35 AM, Nelson A. de Oliveira wrote: > If I did it right, it should appear as "Debian Med" Already updated. It's there! :-) -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact

Re: Blog about Debian Med BOF

2011-08-03 Thread Nelson A. de Oliveira
Hi! On Wed, Aug 3, 2011 at 8:21 AM, Andreas Tille wrote: > As a planet.d.o ignorant I can not give good advise here.  If the usual > Blogs are issued by *persons* the "Debian Med Team" is probably matching > this person-approach.  If also *projects* are posting there any of the > above suggestion

Re: Blog about Debian Med BOF

2011-08-03 Thread Nelson A. de Oliveira
On Wed, Aug 3, 2011 at 8:11 AM, Nelson A. de Oliveira wrote: > The name that will appear on Planet is better as "Debian Med" or > "Debian in Biology and Medicine"? Or "Debian Med Team" or a better name :-) Best regards, Nelson -- To UNSUBSCRIBE, email to

Re: Blog about Debian Med BOF

2011-08-03 Thread Nelson A. de Oliveira
Hi! On Wed, Aug 3, 2011 at 6:26 AM, Andreas Tille wrote: > BTW, is there anybody who might care for including the Debian Med blog > into planet.debian.org? The name that will appear on Planet is better as "Debian Med" or "Debian in Biology and Medicine"? Best regards, Nelson -- To UNSUBSCRIB

Re: Locked files in our SVN repository

2011-07-18 Thread Nelson A. de Oliveira
On Mon, Jul 18, 2011 at 11:36 AM, Nelson A. de Oliveira wrote: > Am I missing something or it's lack of caffeine? As always, the problem is the stupid user :-) It seems that files were locked due to an interrupted "svn update" (thus needing a "svn cleanup") B

Locked files in our SVN repository

2011-07-18 Thread Nelson A. de Oliveira
Hi! I did a new checkout from our SVN repository (svn checkout svn+ssh://nao...@svn.debian.org/svn/debian-med/trunk) to update raster3d but I saw that all files are locked. Am I missing something or it's lack of caffeine? Thank you! Best regards, Nelson -- To UNSUBSCRIBE, email to debian-med

Re: rev 6863 (Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6)

2011-05-30 Thread Nelson A. de Oliveira
Hi! On Mon, May 30, 2011 at 6:07 PM, Thorsten Alteholz wrote: > There are about 1800 files to be checked. > Are there any tools to make this task a bit easier? licensecheck (from the devscripts package) can help you, but it's still highly recommended to manually review all the files (there are c

Re: smile

2011-05-20 Thread Nelson A. de Oliveira
Hi! On Fri, May 20, 2011 at 6:49 PM, Thorsten Alteholz wrote: > PS: Does anybody know of problems with alioth? All my connections are > refused. Wouldn't this be a nice opportunity for a tweet? http://lists.debian.org/debian-infrastructure-announce/2011/05/msg0.html ;-) Best regards, Nelso

Re: Please proofread paper

2010-12-10 Thread Nelson A. de Oliveira
Hi! On Fri, Dec 10, 2010 at 11:18 AM, Nicolas Barbier wrote: > Patch for paper-text.tex attached. I have commited your changes, thank you! Best regards, Nelson -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.d

Re: Please proofread paper

2010-12-09 Thread Nelson A. de Oliveira
On Fri, Dec 10, 2010 at 12:08 AM, Michael Hanke wrote: > I committed another set of changes, but then started to conflict with > 'naoliv' and stopped for now. When is the final deadline? Sorry :-( I did finish the typos that I found, however, so there won't be any more conflicts caused by me. B

Re: [Debian-med-packaging] Bug#594860: Bug#594860: Bug#594860: Workaround for #594860

2010-10-24 Thread Nelson A. de Oliveira
Hi Steffen! On Sun, Oct 24, 2010 at 10:57 PM, Steffen Möller wrote: > Hi Gregor, have many thanks! I'll upload later tonight. Note that on i386, kfreebsd-i386 and hurd-i386 it should be patched to don't use SSE too. See http://lists.debian.org/debian-med/2010/09/msg00062.html Best regards, Nels

Re: OpenMRS package is ready, I believe

2010-09-28 Thread Nelson A. de Oliveira
Hi Misha! On Tue, Sep 28, 2010 at 11:06 PM, misha680 wrote: > Here is a link to the uploaded package: > http://www.2shared.com/file/SeV8AGVg/openmrs_161-1_all.html The binary packages (.deb files) aren't usefull for review. We need the .dsc, .orig.tar.gz (or .orig.tar.bz2) and the .diff.gz (.deb

Re: Compile flags for hmmer

2010-09-27 Thread Nelson A. de Oliveira
Hi again! On Mon, Sep 27, 2010 at 3:05 PM, Nelson A. de Oliveira wrote: > Still about the compiler flags for hmmer (#594860), on i386 [1] and > kfreebsd-i386 [2] it's being used the SSE implementation (compiled > with -msse2). Also on hurd-i386 (from https://buildd.debian.org/stat

Compile flags for hmmer

2010-09-27 Thread Nelson A. de Oliveira
Hi! Still about the compiler flags for hmmer (#594860), on i386 [1] and kfreebsd-i386 [2] it's being used the SSE implementation (compiled with -msse2). While it's almost sure that people who use hmmer have processors >= Pentium 4 and Athlon 64, there is still a small probability that some users

Re: [med-svn] r4993 - trunk/community/website

2010-07-02 Thread Nelson A. de Oliveira
Hi Steffen! On Fri, Jul 2, 2010 at 1:41 PM, Steffen Möller wrote: > this has fixed the first problem. Now another one surfaced. Now it should be clean it seems. Can you retest it only to confirm, please? Best regards, Nelson -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with

Re: some broke our website

2010-07-02 Thread Nelson A. de Oliveira
Hi Steffen! On Fri, Jul 2, 2010 at 1:14 PM, Steffen Möller wrote: > It is the very same, still. I think it is just the … that it > complains about. Removed all the ellipsis entries (they weren't necessary, but indeed it would be better to use … instead …) Can you do a new test? Best regards, Ne

Re: some broke our website

2010-07-02 Thread Nelson A. de Oliveira
Hi! (It wasn't me who broke it) It works nicely here on Chomium, Opera and Iceweasel. But indeed, it fails to validate with the W3C validator. I have removed one php close tag (that was wrong). Steffen, can you see if it still fails on Firefox, please? Best regards, Nelson -- To UNSUBSCRIBE,

Re: [Debian-med-packaging] Bug#565004: insighttoolkit: ftbfs with gcc-4.5

2010-01-12 Thread Nelson A. de Oliveira
Hi! On Tue, Jan 12, 2010 at 11:04 PM, Matthias Klose wrote: > /usr/include/c++/4.5/bits/stl_uninitialized.h: In function 'void > std::__uninitialized_construct_range(_ForwardIterator, _ForwardIterator, > _Tp&)': > /usr/include/c++/4.5/bits/stl_uninitialized.h:231: error: a function call > cann

Re: [Debian-med-packaging] dicomscope_3.6.0-1_i386.changes REJECTED

2009-12-17 Thread Nelson A. de Oliveira
Hi! On Thu, Dec 17, 2009 at 8:13 PM, Barry deFreese wrote: > Ah, if the pdfs were generated from the source then that is OK and is my > mistake.  The lut files sound OK too.  If those were the only two binary file > types, we should be OK, just re-upload and I will fast-track it. Just a suggesti

Re: Pending upload: dicomscope / pixelmed

2009-12-14 Thread Nelson A. de Oliveira
On Mon, Dec 14, 2009 at 1:37 PM, Mathieu Malaterre wrote: >  Does anyone knows if there is something particular going on with NEW > package ? dicomscope/pixelmed have not been uploaded (submitted ~3 > weeks ago). Actually it can take months (so 3 week is normal) to new packages be processed. It o

Typo in phyml version number?

2009-10-07 Thread Nelson A. de Oliveira
Hi! While fixing the watch file of phyml, I saw that its version number in debian/changelog is 200900706 while upstream version is 20090706 (there is one more zero on our version number). Is this a typo? Best regards, Nelson -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with

Re: ncbi-tools onder Debian Med group maintenance?

2009-09-28 Thread Nelson A. de Oliveira
Hi! On Tue, Sep 29, 2009 at 12:08 AM, Aaron M. Ucko wrote: > Great; thanks!  I have been tracking full history in a private svn > repository, so I'll be wanting to convert that to git; any tips on > doing so? See the package git-svn Best regards, Nelson -- To UNSUBSCRIBE, email to debian-med-

Re: problem with debian-med list

2009-09-28 Thread Nelson A. de Oliveira
Hi! On Mon, Sep 28, 2009 at 12:31 PM, Eric MAEKER wrote: > But 'svn checkout svn+ssh://svn.debian.org/svn/debian-med/trunk' ask me to > type a password and does not reconize it. It seems that you are missing your username: svn co svn+ssh://ericmaeker-gu...@svn.debian.org/svn/debian-med/trunk/

Re: dicom3tools issues ...

2009-09-08 Thread Nelson A. de Oliveira
Hi! On Tue, Sep 8, 2009 at 10:25 AM, Mathieu Malaterre wrote: > nawk: cannot open "/dev/tty" for output (No such device or address) Wild guess is that it's a problem with awk. Take a look at http://www.gnu.org/manual/gawk/html_node/Special-FD.html It seems to be caused by how awk is using the red

Re: dicom3tools issues ...

2009-09-08 Thread Nelson A. de Oliveira
Hi! On Tue, Sep 8, 2009 at 6:19 AM, Mathieu Malaterre wrote: >  I am looking at the list file contained in dicom3tools and it seems > I am missing the binaries (dciodvfy, dctable...) ! > >  I tried duplicating the issue here but I cannot (*). Is there an > issue with the shell script in rules file

Re: dicom3tools: piuparts question

2009-09-03 Thread Nelson A. de Oliveira
Hi! On Thu, Sep 3, 2009 at 1:34 PM, Mathieu Malaterre wrote: >  I am starring at the puiparts right now, I have been reading the FAQ > but I still do not understand what this means: > > http://piuparts.debian.org/sid/source/d/dicom3tools.html > >  Could someone please let me know what the actual p

Re: dicom3tools_1.0~20090716-2_amd64.changes REJECTED

2009-08-09 Thread Nelson A. de Oliveira
Hi! On Sun, Aug 9, 2009 at 8:52 AM, Mathieu Malaterre wrote: > Could someone let me know what is happening. > (...) > Rejected: md5sum for > /srv/ftp.debian.org/queue/new/dicom3tools_1.0~20090716.orig.tar.gz > doesn't match dicom3tools_1.0~20090716-2.dsc. Probably you are using a different gzip v

Re: Slight issue with dicom3tools

2009-08-08 Thread Nelson A. de Oliveira
Hi! On Sat, Aug 8, 2009 at 11:56 PM, Steve M. Robbins wrote: > The package is still in NEW, but I believe you can make a second > upload of the same revision and it will be overwritten.  If that > doesn't work, you can definitely make a revision -2 upload; both will > appear in the NEW queue and s

Re: pvrg sponsoring

2009-08-07 Thread Nelson A. de Oliveira
Hi! On Fri, Aug 7, 2009 at 12:32 PM, Mathieu Malaterre wrote: >> It seems that since I rename pvrg into pvrg-jpeg, the ITP is not being >> taken into account properly... >> Do I need to do something ? > > Hum, I realize that pvrg-jpeg was uploaded as experimental maybe this > is why the ITP is not

Re: dicom3tools: Upload ?

2009-08-07 Thread Nelson A. de Oliveira
Hi! On Fri, Aug 7, 2009 at 9:36 AM, Mathieu Malaterre wrote: > Everything should have been taken care of. Uploaded, with some fixes too (http://lists.alioth.debian.org/pipermail/debian-med-commit/2009-August/003853.html). Thank you. Best regards, Nelson -- To UNSUBSCRIBE, email to debian-med-

Re: pvrg sponsoring

2009-08-07 Thread Nelson A. de Oliveira
Hi! On Fri, Aug 7, 2009 at 6:47 AM, Mathieu Malaterre wrote: > Should be all done. I tried compiling with gcc-snapshot and it > compiled ok (tons of warnings though). Just committed two small fixes and uploaded it. Thank you! Best regards, Nelson -- To UNSUBSCRIBE, email to debian-med-requ...

Re: dicom3tools: Upload ?

2009-07-29 Thread Nelson A. de Oliveira
Hi! On Wed, Jul 29, 2009 at 9:47 AM, wrote: >  dicom3tools is now completely lintian clean from warning. Anyone to sponsor > the upload ? Almost :-) Still needs to see: W: dicom3tools source: dh-clean-k-is-deprecated W: dicom3tools source: out-of-date-standards-version 3.8.0 (current is 3.8.2)

Re: post-inst message for autodock

2009-07-28 Thread Nelson A. de Oliveira
Hi! On Tue, Jul 28, 2009 at 1:59 PM, Andreas Tille wrote: > On Tue, Jul 28, 2009 at 05:16:46PM +0200, Steffen Moeller wrote: >> in the sake of our group maintenance I want to inform you about a somewhat >> unusual >> post-inst message that I had added to the autodock package, toinform the >> use

Re: dicom3tools: lintian reports no error

2009-07-22 Thread Nelson A. de Oliveira
Hi! On Wed, Jul 22, 2009 at 12:47 PM, Mathieu Malaterre wrote: >  Could someone (a DD) please review my dicom3tools package. Lintian > does not report any error anymore now. There are some warnings when checking the version on svn (with debian/changelog entry from Fri, 17 Jul 2009 14:58:37) See t

Re: MUMmer patches and Artistic license.

2009-07-04 Thread Nelson A. de Oliveira
Hi Charles! On Sat, Jul 4, 2009 at 9:06 AM, Charles Plessy wrote: > we have a patch in the Debian package mummer for which we lost origin and > detailed description. I would like to forward it upstream, but I would prefer > to know what it does before ;) Would somebody have a few minutes to throw

Re: pvrg sponsoring

2009-06-19 Thread Nelson A. de Oliveira
Hi! On Fri, Jun 19, 2009 at 9:27 AM, Mathieu Malaterre wrote: >  Could someone please sponsor the pvrg package, I have cleanup the > remaining lintian issues. Not fully clean :-) See the attached lintian output. Wouldn't it be better to have the source package and the binary package as "pvrg-jpe

Re: [med-svn] r3446 - trunk/packages/gdcm/trunk/debian

2009-05-30 Thread Nelson A. de Oliveira
Hi Mathieu! On Sat, May 30, 2009 at 11:19 AM, Mathieu Malaterre wrote: > Modified: trunk/packages/gdcm/trunk/debian/control > === > --- trunk/packages/gdcm/trunk/debian/control    2009-05-29 05:26:09 UTC (rev > 3445) > +++ trunk/pac

Re: ElementalClinic Debian/Ubuntu

2009-03-11 Thread Nelson A. de Oliveira
Hi! On Wed, Mar 11, 2009 at 10:06 AM, Andreas Tille wrote: > On Wed, 11 Mar 2009, Sebastian Hilbert wrote: > >> This link might be of interest . >> >> https://svn.opensourcery.com/public/elementalclinic/trunk/docs/DEBIAN >> >> from packaging perspective. > > At least not for me because I can not

Re: [med-svn] r2574 - trunk/packages/biococoa/trunk/debian

2008-10-27 Thread Nelson A. de Oliveira
Hi! On Sun, Oct 26, 2008 at 8:48 PM, Scott Christley <[EMAIL PROTECTED]> wrote: > I think biococoa and sequenceconverter.app are ready for upload! biococoa is failing to build: $ pdebuild dpkg-buildpackage: set CFLAGS to default value: -g -O2 dpkg-buildpackage: set CPPFLAGS to default value: dpk

Mustang on Debian

2008-08-03 Thread Nelson A. de Oliveira
Hi! On Sun, Aug 3, 2008 at 8:54 PM, <[EMAIL PROTECTED]> wrote: > Added: > trunk/packages/mustang/trunk/debian/patches/04-gcc-4.3-exit > Modified: > trunk/packages/mustang/trunk/debian/changelog > trunk/packages/mustang/trunk/debian/control > trunk/packages/mustang/trunk/debian/patches/00l

Re: [med-svn] r2366 - in trunk/packages/maq/trunk/debian: . patches

2008-07-30 Thread Nelson A. de Oliveira
Hi! On Wed, Jul 30, 2008 at 9:52 AM, <[EMAIL PROTECTED]> wrote: > -Description: maps short fixed-legth polymporphic DNA sequence reads to > reference sequences > +Description: maps short fixed-legth polymorphic DNA sequence reads to > reference sequences Isn't it fixed-length? (missing a N) B

Re: Bug#487026: ITP: velvet -- Sequence assembler for very short reads

2008-06-19 Thread Nelson A. de Oliveira
Hi! On Thu, Jun 19, 2008 at 11:40 PM, Charles Plessy <[EMAIL PROTECTED]> wrote: > Basically what I did was to disable the building of local zlib, include > the zlib.h from /usr/include instead of the local one, and add -lm and > -lz to CFLAGS from CDBS. Any idea what -lm and -lz mean? You are lin

Re: RFS: proda - maintainance release

2008-06-11 Thread Nelson A. de Oliveira
Hi David! On Wed, Jun 11, 2008 at 10:11 AM, David Paleino <[EMAIL PROTECTED]> wrote: > Hi all, > I've done some "maintainance" on proda [1] -- I believe it could be uploaded > for > a "maintainance revision". Uploaded, thank you! Best regards, Nelson -- To UNSUBSCRIBE, email to [EMAIL PROTEC

Emails needing an answer

2008-05-10 Thread Nelson A. de Oliveira
Hi my friends! I am sending this message to you because I know that I need to (or will have to) answer/read some of your messages /do something for you. The problem is: I was at the hospital for 8 days (surgery). Before this I was really bad too. So for sure I have a lot of messages to reply, real

Re: New Debian maintainer Charles Plessy

2008-04-18 Thread Nelson A. de Oliveira
Ha! :-D On Fri, Apr 18, 2008 at 1:02 AM, Charles Plessy <[EMAIL PROTECTED]> wrote: > this is a great day for me and I would like to give a big THANK YOU to > everybody who made it possible. Special thanks to Andreas Tille, my > advocate, Christoph Berg, my AM, and Anìbal Monsalve Salazar, my fi

Re: automatic rebuild of live-cd

2008-04-17 Thread Nelson A. de Oliveira
Hi! On Thu, Apr 17, 2008 at 5:38 AM, Andreas Tille <[EMAIL PROTECTED]> wrote: > The watch file informs the Debian maintainer about new upstream versions. > I have to admit that I failed to get a notice about new upstream versions > for packages I would like to watch. I know that I could run us

Re: [RFS] libbio-mage-perl

2008-04-15 Thread Nelson A. de Oliveira
Hi! On Tue, Apr 15, 2008 at 11:57 AM, Charles Plessy <[EMAIL PROTECTED]> wrote: > OK, it is probably a missing build dep. I will investigate this > tomorrow. Was missing libtie-ixhash-perl :-) I have added it, commited on SVN and uploaded the package. Thank you! Best regards, Nelson -- To

Re: [RFS] libbio-mage-perl

2008-04-15 Thread Nelson A. de Oliveira
Hi! On Mon, Apr 14, 2008 at 11:04 AM, Charles Plessy <[EMAIL PROTECTED]> wrote: > It is in our SVN repo with a watch file for you to upload the original > sources. I am still not yet a DD, so I need somebody to sponsor this > pacakge to NEW. It seems that almost every test is failing here (and

Re: [med-svn] r1733 - trunk/packages/ncbi-epcr/trunk/debian

2008-04-10 Thread Nelson A. de Oliveira
Hi! On Thu, Apr 10, 2008 at 3:24 AM, <[EMAIL PROTECTED]> wrote: > [HELP] Added watch file but this does not work. :-(( Any clue? It's working here: $ uscan --report-status Processing watchfile line for package epcr... Newest version on remote site is 2.3.9, local version is 1.2.0 epcr: Newer v

Re: Bioperl ready for upload.

2008-04-08 Thread Nelson A. de Oliveira
Hi! On Tue, Apr 8, 2008 at 2:35 AM, Charles Plessy <[EMAIL PROTECTED]> wrote: > My pbuilder is borken and I had no time to learn sbuild. Can somebody > upload bioperl? The main changes are: Somebody has uploaded it :-) Thank you! Best regards, Nelson -- To UNSUBSCRIBE, email to [EMAIL PROTEC

Re: clustalw-mpi: new upstream release and watch file.

2008-04-07 Thread Nelson A. de Oliveira
Hi! On Mon, Apr 7, 2008 at 9:46 PM, Charles Plessy <[EMAIL PROTECTED]> wrote: > I tried to add a watch file to clustalw-mpi, but did not manage to make > one that works. Can somebody have a look? I am affraid that the problem > is trivial but I am blind to it. You missed "./" :-) > If this i

Re: Suppression of pkg-emboss.

2008-03-10 Thread Nelson A. de Oliveira
Hi! On Mon, Mar 10, 2008 at 11:14 PM, Charles Plessy <[EMAIL PROTECTED]> wrote: > What shall we do for the mailing lists? Just delete? I do not mind this > but I do not feel like taking the decision alone. I agree with whatever you choose ;-) Best regards, Nelson -- To UNSUBSCRIBE, email to

Re: [RFS] clustalw.

2008-03-09 Thread Nelson A. de Oliveira
Hi Charles! On Sun, Mar 9, 2008 at 10:44 AM, Charles Plessy <[EMAIL PROTECTED]> wrote: > The clustalw package is ready for upload. There has been a new upstream > release this week, in which a new option has been introduced > (-fullhelp). Also, Clustal packages have a new home, www.clustal.org.

Re: [med-svn] r1515 - trunk/packages/seaview/trunk/debian

2008-03-05 Thread Nelson A. de Oliveira
Hi Charles! On Wed, Mar 5, 2008 at 9:51 AM, <[EMAIL PROTECTED]> wrote: > Log: > Bumped copyrights to 2008 I have already uploaded it :-( -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]

Re: AutoDock - comments on packaging, please.

2008-02-29 Thread Nelson A. de Oliveira
Hi! On Fri, Feb 29, 2008 at 7:28 PM, Andreas Tille <[EMAIL PROTECTED]> wrote: > On Fri, 29 Feb 2008, Daniel Leidert wrote: > > > - very important: grep for License, Copyright and Public Domain strings > > to make sure, your debian/copyright is complete - incomplete > > debian/copyright are most

Re: pngquant (Was: amap-align, boxshade and dialign ready for upload?)

2008-02-25 Thread Nelson A. de Oliveira
Hi! On Mon, Feb 25, 2008 at 7:15 AM, Andreas Tille <[EMAIL PROTECTED]> wrote: > On Sun, 24 Feb 2008, Nelson A. de Oliveira wrote: > > If I did everything correctly, they are ready to be uploaded (and I > > will upload them after one more review). Please, see if there i

Re: [RFS] clustalx version 1.83

2008-02-25 Thread Nelson A. de Oliveira
Hi! > On Mon, Feb 25, 2008 at 4:19 AM, Charles Plessy > > clustalx is ready, but clustalw is not yet lintian-clean. Nevertheless, > > clustalx will have to go to NEW, so I guess it will not hurt if it is > > uploaded a bit before clustalw. Hum... directly on incoming :-) Nelson -- To UN

Re: [RFS] clustalx version 1.83

2008-02-25 Thread Nelson A. de Oliveira
Hi Charles! On Mon, Feb 25, 2008 at 4:19 AM, Charles Plessy <[EMAIL PROTECTED]> wrote: > clustalx is ready, but clustalw is not yet lintian-clean. Nevertheless, > clustalx will have to go to NEW, so I guess it will not hurt if it is > uploaded a bit before clustalw. Uploaded. I just hope that

Re: RFS: primer3

2008-02-25 Thread Nelson A. de Oliveira
Hi! On Mon, Feb 25, 2008 at 4:33 AM, Charles Plessy <[EMAIL PROTECTED]> wrote: > There is a new upstream release of primer3 that fixes a bug reported in > Ubuntu (https://bugs.launchpad.net/ubuntu/+source/primer3/+bug/191053). There. Thank you! Best regards, Nelson -- To UNSUBSCRIBE, email

Re: amap-align, boxshade and dialign ready for upload?

2008-02-23 Thread Nelson A. de Oliveira
Hi! On Tue, Feb 19, 2008 at 4:58 AM, Andreas Tille <[EMAIL PROTECTED]> wrote: > On Mon, 18 Feb 2008, Nelson A. de Oliveira wrote: > > > Give me one week and I will commit gff2ps, gff2aplot, gdpc, raster3d, > > biofox and biosquid to our repository. > > OK, one wee

Re: [RFS] clustalx version 1.83

2008-02-21 Thread Nelson A. de Oliveira
Hi! On Fri, Feb 22, 2008 at 12:04 AM, Charles Plessy <[EMAIL PROTECTED]> wrote: > > Uploading clustalw (only building clustalw) and clustalx (only > > building clustalx), both as 1.83-4 will do the job as I can see (and > > won't cause any problems). > > There is no problem in not uploading a

Re: [RFS] clustalx version 1.83

2008-02-21 Thread Nelson A. de Oliveira
Hi! On Thu, Feb 21, 2008 at 9:51 PM, Charles Plessy <[EMAIL PROTECTED]> wrote: > > Why not only use 1.83-4? It will replace the one already available. > > It is a new package, I do not know if it would work… Doesn't it need to > end by -1? Otherwise, this would be obviously the thing to do. Up

Re: [RFS] clustalx version 1.83

2008-02-21 Thread Nelson A. de Oliveira
Hi Charles! On Thu, Feb 21, 2008 at 9:39 PM, Charles Plessy <[EMAIL PROTECTED]> wrote: > > I have just one doubt about the process: there are already binary > > packages for clustalx 1.83 in non-free. Will they be overwritten or will > > they cause a problem? > > Actually, I think that the bes

Re: amap-align, boxshade and dialign ready for upload?

2008-02-18 Thread Nelson A. de Oliveira
Hi! On Feb 18, 2008 6:01 AM, Andreas Tille <[EMAIL PROTECTED]> wrote: > Another issues are biosquid and clustalw-mpi - could we start > Group maintenance here? I'm also personally guilty for some > packages not yet in the SVN reporitory - I'm working on it. Give me one week and I will commit gff

Re: Using alioth

2008-02-13 Thread Nelson A. de Oliveira
Hi! On Feb 13, 2008 5:20 AM, David Paleino <[EMAIL PROTECTED]> wrote: > SSHing, and checking, here's what happened: > > $ ls -lah bugs.php ddtp.php > -rw-rw-r--+ 1 naoliv debian-med 37K 2008-02-13 08:20 bugs.php > -rw-rw-r--+ 1 naoliv debian-med 160K 2008-02-13 08:20 ddtp.php > $ > > What's the m

Re: [RFS] muscle

2008-02-11 Thread Nelson A. de Oliveira
Hi again! 2008/2/11 Nelson A. de Oliveira <[EMAIL PROTECTED]>: > Hum... > I created the compat file because I saw this message while building muscle: > > dh_clean: Compatibility levels before 4 are deprecated. > > But looking at the log there is an "echo 5 >debi

Re: [RFS] muscle

2008-02-11 Thread Nelson A. de Oliveira
Hi! On Feb 11, 2008 10:46 AM, David Paleino <[EMAIL PROTECTED]> wrote: > Here it is talking about _documentation_ referring to latest compatibility > level. It does not say that CDBS uses the highest compatibility level > available. Or did I miss something? On Feb 11, 2008 10:50 AM, Andreas Tille

Re: Using CDBS (was: Re: [RFS] muscle)

2008-02-11 Thread Nelson A. de Oliveira
Hi! On Feb 11, 2008 10:40 AM, David Paleino <[EMAIL PROTECTED]> wrote: > Il giorno Mon, 11 Feb 2008 20:51:25 +0900 > Charles Plessy <[EMAIL PROTECTED]> ha scritto: > > > (By the way, I am swiching a lot of packages to CDBS; if it is an issue, > > I am of course open to discussion. I am usually doi

Re: [RFS] muscle

2008-02-11 Thread Nelson A. de Oliveira
Hi! On Feb 11, 2008 10:16 AM, Andreas Tille <[EMAIL PROTECTED]> wrote: > On Mon, 11 Feb 2008, Charles Plessy wrote: > > > Actually, I tend to remove debian/compat in the packages using CDBS, > > because in that case it uses the highest value available, thus solving > > the backporting issues. > >

Re: [RFS] muscle

2008-02-11 Thread Nelson A. de Oliveira
Hi! On Feb 11, 2008 9:51 AM, Charles Plessy <[EMAIL PROTECTED]> wrote: > Hi Nelson, thank you for the upload. You are welcome. > Actually, I tend to remove debian/compat in the packages using CDBS, > because in that case it uses the highest value available, thus solving > the backporting issues.

Re: [RFS] muscle

2008-02-09 Thread Nelson A. de Oliveira
Hi Charles! On Feb 9, 2008 7:24 AM, Charles Plessy <[EMAIL PROTECTED]> wrote: > I have packaged a new upstream release of muscle, a program for multiple > sequence alignment. It fixes a building bug when GCC 4.3 is used, and as > for mustang, the name of the upstream tarball was not changed for th

Re: Mustang, please sponsor

2008-02-06 Thread Nelson A. de Oliveira
Hi! On Feb 6, 2008 11:12 PM, Morten Kjeldgaard <[EMAIL PROTECTED]> wrote: > The patch file applies without problems to tarball 883bd...etc... so > that is the one we should build against. I simply wrapped the > patchfile "patch_15Jan2008.mustang" with a dpatch header and called > it 01-upstream.dp

Re: Mustang, please sponsor

2008-02-06 Thread Nelson A. de Oliveira
Hi! On Feb 6, 2008 9:06 PM, Morten Kjeldgaard <[EMAIL PROTECTED]> wrote: > On 06/02/2008, at 20.19, Nelson A. de Oliveira wrote: > > > You need to use 3.0+p1 only if you use the new tarball. > > With the old one the version will be 3.0 only. > > Of course! It makes

Re: Mustang, please sponsor

2008-02-06 Thread Nelson A. de Oliveira
Hi! On Feb 6, 2008 6:08 PM, Andreas Tille <[EMAIL PROTECTED]> wrote: > On Wed, 6 Feb 2008, Nelson A. de Oliveira wrote: > > > I keep my "old tarball + patch = 3.0-1, new tarball = 3.0+p1-1" :-) > > But lets see what the other members of the list have to say

Re: Mustang, please sponsor

2008-02-06 Thread Nelson A. de Oliveira
Hi! On Feb 6, 2008 4:23 PM, Morten Kjeldgaard <[EMAIL PROTECTED]> wrote: > On 05/02/2008, at 16.37, Nelson A. de Oliveira wrote: > > Agreed? :-) > > Heh, not quite actually... :-) That's good ;-) > The way I've done it is apply upstreams patches via the dpatch

Re: Mustang, please sponsor

2008-02-05 Thread Nelson A. de Oliveira
Hi! On Feb 5, 2008 6:49 AM, Morten Kjeldgaard <[EMAIL PROTECTED]> wrote: > There is no new tarball. There's only a patch file on upstream's web > site that can be applied to the "old" tarball. I've wrapped that into > a dpatch, so it is necessary to mark that in the version number I > think. Vers

Re: Mustang, please sponsor

2008-02-04 Thread Nelson A. de Oliveira
Hi Morten! On Feb 4, 2008 10:36 AM, Morten Kjeldgaard <[EMAIL PROTECTED]> wrote: > First, the sources have been patched with a patch from upstream. > Unfortunately, upstream has not changed the version number. > Therefore, the patch level has been added to the release. I don't > know if this is in

Re: [RFS] TreeView X

2008-01-31 Thread Nelson A. de Oliveira
Hi! On Jan 31, 2008 2:22 AM, Charles Plessy <[EMAIL PROTECTED]> wrote: > Here is the full changelog. Can somebody upload the package ? Yep :-) Thank you! Best regards, Nelson -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]

Re: [RFS] Please sponsor glam2.

2008-01-29 Thread Nelson A. de Oliveira
Hi Charles! On Jan 29, 2008 12:30 PM, Charles Plessy <[EMAIL PROTECTED]> wrote: > Steffen and I have packaged glam2, a motif-detection software for > biological sequences. For this package, I have made use of CDBS, so that > debian/rules is trivial. I had to patch the manpages to let them accept >

Re: Debian-med cited on an article of LWN

2008-01-29 Thread Nelson A. de Oliveira
Hi again! I saw now that there is a nice mechanism to generate an URL of a subscriber only article, so people can read it: http://lwn.net/SubscriberLink/266712/b62a713379dc92f1/ Good reading. Best regards, Nelson -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe".

Re: Group policy draft

2008-01-29 Thread Nelson A. de Oliveira
Hi people! 2008/1/29 David Paleino <[EMAIL PROTECTED]>: > as you might have seen, r1213 introduces a "Group Policy". As many other teams > have one, I felt the need of writing one for us. Consider it still a draft > (anyone knows Foo Bar? ;) ), it can be improved in many ways. Good! > Suggestion

Debian-med cited on an article of LWN

2008-01-29 Thread Nelson A. de Oliveira
Hi! I don't know if somebody saw this, but we have been cited on http://lwn.net/Articles/266712/ It's a subscriber-only content (Debian Developers who are part of the Debian Project group at LWN can read it). On day 31 it will be open for everyone. It's a small note, but we are there (sorry if t

Re: [RFS] emboss

2008-01-28 Thread Nelson A. de Oliveira
Hi Charles! On Jan 27, 2008 11:39 PM, Charles Plessy <[EMAIL PROTECTED]> wrote: > As you know I made a typo that makes the packages uploaded with > XS-DM-Upload-Allowed: Yes unavailable for DM upload (it should be 'yes', > in lower case). I just corrected this in our SVN. Hum... maybe a wishlist

Re: SVN checkin

2008-01-12 Thread Nelson A. de Oliveira
Hi! On Jan 12, 2008 1:11 AM, Charles Plessy <[EMAIL PROTECTED]> wrote: > > On Jan 12, 2008 12:13 AM, Nelson A. de Oliveira <[EMAIL PROTECTED]> wrote: > > > And I was thinking if it's not better to use /tmp/mustang (instead > > > only mustang) in

Re: please sponsor muscle_3.70-1

2008-01-12 Thread Nelson A. de Oliveira
Hi! On Jan 12, 2008 6:22 AM, Charles Plessy <[EMAIL PROTECTED]> wrote: > In addition, the packaging has been extensively tidied by me, Nelson and > David, and the upload would fix a Debian bug (the nostrip option was not > handled). Extensively only applies to Charles and David ;-) > Can somebod

Re: SVN checkin

2008-01-11 Thread Nelson A. de Oliveira
On Jan 12, 2008 12:13 AM, Nelson A. de Oliveira <[EMAIL PROTECTED]> wrote: > And I was thinking if it's not better to use /tmp/mustang (instead > only mustang) in debian/runtest and debian/patches/test_zf-cchh.dpatch ^^^ Instead only /tmp, sorry Nelson -- To U

Re: SVN checkin

2008-01-11 Thread Nelson A. de Oliveira
Hi Morten! On Jan 11, 2008 2:59 PM, Morten Kjeldgaard <[EMAIL PROTECTED]> wrote: > Regarding mustang, it is lintian clean, it "just works", and I do consider > it ready for upload. (Of course I can't promise it's without bugs, but the > program has been available through Ubuntu 7.10 for some month

Re: Please sponsor embassy-domalign and embassy-domainatrix

2008-01-10 Thread Nelson A. de Oliveira
Hi! On Jan 10, 2008 10:29 PM, Charles Plessy <[EMAIL PROTECTED]> wrote: > Well, if we open ITPs, then we should wait a few days for feedback > before uploading. But these packages are small and not so complex; I > think that we can proceed without ITPs. So both uploaded :-) Thank you! Best rega

Re: Please sponsor embassy-domalign and embassy-domainatrix

2008-01-10 Thread Nelson A. de Oliveira
Hi again! On Jan 10, 2008 9:57 PM, Nelson A. de Oliveira <[EMAIL PROTECTED]> wrote: > embassy-domainatrix is failing to build here (and I am using latest emboss): Could you verify my commit? It seems to build fine now, but I have doubt if it's libgd2-noxpm-dev or libgd2-xpm-dev

Re: Please sponsor embassy-domalign and embassy-domainatrix

2008-01-10 Thread Nelson A. de Oliveira
Hi Charles! On Jan 10, 2008 9:53 PM, Charles Plessy <[EMAIL PROTECTED]> wrote: > Le Fri, Jan 11, 2008 at 08:47:32AM +0900, Charles Plessy a écrit : > > > > The package names are: > > - embassy-domainatrix > > - embassy-domalign > > I forgot to say that they need emboss 5.0.0-3 to pbuild correctl

Re: Updated emboss package including new upstream patch.

2008-01-10 Thread Nelson A. de Oliveira
Hi Charles! On Jan 10, 2008 11:10 AM, Charles Plessy <[EMAIL PROTECTED]> wrote: > I took the opportunity to tidy it a bit, and to transfer it to > Debian-Med. Can somebody upload it? Here is the changelog: Uploaded. Thank you for your work! Best regards, Nelson -- To UNSUBSCRIBE, email to [E

Re: Can somebody upload the latest probcons from the svn ?

2008-01-04 Thread Nelson A. de Oliveira
Hi again! On Jan 4, 2008 2:05 PM, Nelson A. de Oliveira <[EMAIL PROTECTED]> wrote: > Hi Charles! > > On Jan 4, 2008 2:03 PM, Charles Plessy <[EMAIL PROTECTED]> wrote: > > I got a bug report this morning: probcons ships a broken version of the > > probcons-RNA pr

Re: Can somebody upload the latest probcons from the svn ?

2008-01-04 Thread Nelson A. de Oliveira
Hi Charles! On Jan 4, 2008 2:03 PM, Charles Plessy <[EMAIL PROTECTED]> wrote: > I got a bug report this morning: probcons ships a broken version of the > probcons-RNA program. I corrected the problem in our SVN. Can somebody > upload the package ? It also contain other improvements: Just a moment

Re: fixed Bug#457921: t-coffee: packaging bug

2007-12-29 Thread Nelson A. de Oliveira
Hi Charles! On Dec 29, 2007 4:07 PM, Charles Plessy <[EMAIL PROTECTED]> wrote: > I think I have fixed bug 457921, in which binary-indep was also > producing binary-arch packages, and vice versa. The fix is not elegant, > so if somebody know a better way, please tell me ! Here is the > changelog, a

Re: [med-svn] Needed fields for update-tasks (was: Re: r1010 - trunk/community/website)

2007-12-24 Thread Nelson A. de Oliveira
Hi David! On Dec 24, 2007 1:38 PM, David Paleino <[EMAIL PROTECTED]> wrote: > I'd like to file a bug to for adding a License: field to the > binary sections (I mean those that shows up with "apt-cache show foo"). That > would help automated scripts, like ours. Where should I file that? dpkg But

  1   2   >