Re: Latest blog post

2011-08-22 Thread Nelson A. de Oliveira
Hi! On Mon, Aug 22, 2011 at 12:34 PM, Steffen Möller steffen_moel...@gmx.de 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

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,

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 domi...@debian.org 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

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 domi...@debian.org 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

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 andr...@an3as.eu 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

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 nao...@gmail.com 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 debian-med-requ

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 andr...@an3as.eu 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

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 nao...@gmail.com 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 listmas

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

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 nao...@gmail.com 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) Best regards, Nelson

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 debian-...@alteholz.de 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

Re: smile

2011-05-20 Thread Nelson A. de Oliveira
Hi! On Fri, May 20, 2011 at 6:49 PM, Thorsten Alteholz debian-...@alteholz.de 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 ;-)

Re: Please proofread paper

2010-12-10 Thread Nelson A. de Oliveira
Hi! On Fri, Dec 10, 2010 at 11:18 AM, Nicolas Barbier nicolas.barb...@gmail.com 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?

Re: Please proofread paper

2010-12-09 Thread Nelson A. de Oliveira
On Fri, Dec 10, 2010 at 12:08 AM, Michael Hanke m...@debian.org 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

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 steffen_moel...@gmx.de 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

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 misha...@gmail.com 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

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: 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 nao...@gmail.com 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

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

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 steffen_moel...@gmx.de wrote: It is the very same, still. I think it is just the hellip; that it complains about. Removed all the ellipsis entries (they weren't necessary, but indeed it would be better to use #8230; instead hellip;)

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 steffen_moel...@gmx.de 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

Re: Pending upload: dicomscope / pixelmed

2009-12-14 Thread Nelson A. de Oliveira
On Mon, Dec 14, 2009 at 1:37 PM, Mathieu Malaterre mathieu.malate...@gmail.com 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

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: 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 eric.mae...@free.fr 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

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 u...@debian.org 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

Re: dicom3tools issues ...

2009-09-08 Thread Nelson A. de Oliveira
Hi! On Tue, Sep 8, 2009 at 6:19 AM, Mathieu Malaterremathieu.malate...@gmail.com 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

Re: dicom3tools issues ...

2009-09-08 Thread Nelson A. de Oliveira
Hi! On Tue, Sep 8, 2009 at 10:25 AM, Mathieu Malaterremathieu.malate...@gmail.com 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

Re: dicom3tools: piuparts question

2009-09-03 Thread Nelson A. de Oliveira
Hi! On Thu, Sep 3, 2009 at 1:34 PM, Mathieu Malaterremathieu.malate...@gmail.com 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

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 Malaterremathieu.malate...@gmail.com 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

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. Robbinsst...@sumost.ca 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

Re: pvrg sponsoring

2009-08-07 Thread Nelson A. de Oliveira
Hi! On Fri, Aug 7, 2009 at 6:47 AM, Mathieu Malaterremathieu.malate...@gmail.com 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,

Re: dicom3tools: Upload ?

2009-08-07 Thread Nelson A. de Oliveira
Hi! On Fri, Aug 7, 2009 at 9:36 AM, Mathieu Malaterremathieu.malate...@gmail.com 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

Re: pvrg sponsoring

2009-08-07 Thread Nelson A. de Oliveira
Hi! On Fri, Aug 7, 2009 at 12:32 PM, Mathieu Malaterremathieu.malate...@gmail.com 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

Re: dicom3tools: Upload ?

2009-07-29 Thread Nelson A. de Oliveira
Hi! On Wed, Jul 29, 2009 at 9:47 AM, mathieu.malate...@gmail.com 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

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 Malaterremathieu.malate...@gmail.com 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,

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 Plessyple...@debian.org 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

Re: pvrg sponsoring

2009-06-19 Thread Nelson A. de Oliveira
Hi! On Fri, Jun 19, 2009 at 9:27 AM, Mathieu Malaterremathieu.malate...@gmail.com 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

Re: ElementalClinic Debian/Ubuntu

2009-03-11 Thread Nelson A. de Oliveira
Hi! On Wed, Mar 11, 2009 at 10:06 AM, Andreas Tille til...@rki.de 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:

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/00list

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) Best

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 linking

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 PROTECTED] with

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,

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 first

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 uscan

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

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

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: 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 to

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

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 week (not one hour more, trust me

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 best

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.

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 meaning of

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 debian/compat before it starts to build (you can

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: [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. Ah, this is

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 this

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 system to the old tarball. When

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, right? IMHO both things (old tarball + patch

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 absolutely sense! 3.0 it is! I applied

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.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. Version

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]

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

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 bug

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 months now,

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 correctly. In the

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 Best regards

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 regards,

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, and

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 some_package 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?

Re: RFS: proda

2007-12-15 Thread Nelson A. de Oliveira
Hi David! On Dec 15, 2007 11:00 PM, David Paleino [EMAIL PROTECTED] wrote: Hi all, could someone please upload proda (1.0-4) for me? It closes #455269 (FTBFS gcc4.3)... I wish I already was a DM... :@ Uploaded. I have fixed the missing quint in B-D and also updated to Standards Version 3.7.3

Re: It's time for finding a logo

2007-12-07 Thread Nelson A. de Oliveira
Hi! On Dec 7, 2007 9:04 AM, Steffen Moeller [EMAIL PROTECTED] wrote: I admit to like it. With some more skills and gimp-time I'd probably go for the snake to swirl around the Debian swirl and thus demonstrate that one no longer needs that rod. Something like that?

Re: DM application for Charles Plessy

2007-12-05 Thread Nelson A. de Oliveira
Hi! I want to advocate Charles (with GPG key 0xBAFEC7F2) as a DM, while he waits his account to be created. I have sponsored some of his packages and he does a superb job maintaining packages [1] and helping Debian-med. [1]http://qa.debian.org/[EMAIL PROTECTED] Thank you! Best regards, Nelson

Re: Can somebody sponsor non-free/dialign-t-doc_0.2.2-1 ?

2007-11-20 Thread Nelson A. de Oliveira
Hi! On Nov 20, 2007 11:52 AM, Charles Plessy [EMAIL PROTECTED] wrote: I remind you that no file in this package is non-free. The LaTeX sources of the documentation are lacking, but the PDF. PS, and html files themeselves are originally distributed under the LGPL. I understand. And I have

Re: Can somebody sponsor dialign-t_0.2.2.dfsg-1 ?

2007-11-19 Thread Nelson A. de Oliveira
Hi Charles! On Nov 19, 2007 1:24 PM, Charles Plessy [EMAIL PROTECTED] wrote: I have prepared a new version of dialign-t in which I rm-rf'ed the doc directory (I am pessimistic on the outcome of the discussion on -devel, which already digressed into an interesting debate about embedded fonts).

Re: Minor unreported bug fixed on seaview. Can anybody upload ?

2007-11-18 Thread Nelson A. de Oliveira
Hi Charles! On Nov 18, 2007 1:23 PM, Charles Plessy [EMAIL PROTECTED] wrote: I reverted the patch responsible for this. Although the bug is not reported in the BTS, I reproduced it. Can somebody upload the version in the SVN ? By the way, can somebody upload dialign-t ? I think that we

Re: Can somebody sponsor dialign-t

2007-11-14 Thread Nelson A. de Oliveira
Hi Charles! On Nov 14, 2007 2:27 AM, Charles Plessy [EMAIL PROTECTED] wrote: Os is much better than O0, and the temporary loss of performance is in my opinion acceptable. Very good! Do you want that I upload it? And I don't know if you already thought on this, but maybe dialign-t could be

Re: Can somebody sponsor dialign-t

2007-11-14 Thread Nelson A. de Oliveira
Hi! On Nov 14, 2007 9:42 AM, Charles Plessy [EMAIL PROTECTED] wrote: Le Wed, Nov 14, 2007 at 09:26:37AM -0200, Nelson A. de Oliveira a écrit : And I don't know if you already thought on this, but maybe dialign-t could be split into dialign-t and dialign-t-data (lintian says that 98

Re: Can somebody sponsor dialign-t

2007-11-14 Thread Nelson A. de Oliveira
Hi! On Nov 14, 2007 12:41 PM, Charles Plessy [EMAIL PROTECTED] wrote: do not hesitate to send the diff uncompressed when it is so small :) Right :-) -Depends: ${shlibs:Depends}, ${misc:Depends} +Depends: ${shlibs:Depends}, ${misc:Depends}, dialign-t-data (=${source:Version}) Actually,

Re: Can somebody sponsor dialign-t

2007-11-14 Thread Nelson A. de Oliveira
Hi again! On Nov 14, 2007 12:55 PM, Andreas Tille [EMAIL PROTECTED] wrote: On Wed, 14 Nov 2007, Charles Plessy wrote: although I do not expect users to decide to install one without the other. But now I wonder if this fits the renewed interpretation of what Recommends: means, now that

Re: Can somebody sponsor dialign-t and emboss-explorer ?

2007-11-13 Thread Nelson A. de Oliveira
Hi Charles! On Nov 12, 2007 10:54 PM, Charles Plessy [EMAIL PROTECTED] wrote: Le Mon, Nov 12, 2007 at 10:32:20PM -0200, Nelson A. de Oliveira a écrit : (...) gcc -Wall -g -O2 -c -o prob.o prob.c prob.c: In function 'calc_score_dist': prob.c:157: warning: 'sq1' is used uninitialized

Re: Can somebody sponsor dialign-t and emboss-explorer ?

2007-11-13 Thread Nelson A. de Oliveira
Hi again! On Nov 13, 2007 8:34 PM, Nelson A. de Oliveira [EMAIL PROTECTED] wrote: It builds fine if using -O0 Do you want to use -O0 temporarily and upload it? With -Os it also builds fine (-O1 fails) -Os is better than nothing (-O0) Best regards, Nelson -- To UNSUBSCRIBE, email to [EMAIL

Re: Can somebody sponsor dialign-t and emboss-explorer ?

2007-11-12 Thread Nelson A. de Oliveira
Hi Charles! On Nov 12, 2007 12:07 PM, Charles Plessy [EMAIL PROTECTED] wrote: Now that ftp-master is up again, I think that emboss-explorer desserves an update. This one I have uploaded. I have also prepared a new package for dialign-t, a multiple alignment software. Dialign-t does not

Re: Duplicated entry on debian-med page

2007-11-05 Thread Nelson A. de Oliveira
Hi again! On 11/5/07, Nelson A. de Oliveira [EMAIL PROTECTED] wrote: On 11/4/07, David Paleino [EMAIL PROTECTED] wrote: A bug has already been issued: I've added a comment that happens to our repository too: http://code.google.com/p/cia-vc/issues/detail?id=2 Actually revisions 756

Script to verify if we are up-to-date with upstream versions

2007-11-03 Thread Nelson A. de Oliveira
Hi! Below you will see the output of a (very ugly but functional) script that I will run weekly. It will gets latest changelogs and watch files from SVN and verify if we already have the latest upstream version. Up to date packages won't be displayed. What do you think? Suggestions, critics,

Re: Script to verify if we are up-to-date with upstream versions

2007-11-03 Thread Nelson A. de Oliveira
Hi! On 11/4/07, Karsten Hilbert [EMAIL PROTECTED] wrote: Not quite: * gnumed-client: new version available (.0.1-rc5 0.2.7.0) Probably caused by a wrong watch file. See: $ uscan --report-status Processing watchfile line for package gnumed-client... Newest version on remote site is

Re: Please sponsor dialign-t, needed for the meta-aligner dm_coffee.

2007-10-13 Thread Nelson A. de Oliveira
Hi Charles! On 10/13/07, Charles Plessy [EMAIL PROTECTED] wrote: I prepared a package for DIALIGN-T, which is needed by the meta-aligner functions of T-Coffee (m_coffee, dm_coffee). You can find it either in our SVN, or on mentors.d.o: Hum... (...) gcc -Wall -g -O2 -c -o prob.o prob.c

Re: EMBOSS ready for upload to NEW.

2007-10-13 Thread Nelson A. de Oliveira
Hi! On 10/13/07, Charles Plessy [EMAIL PROTECTED] wrote: Not being a DD, I still need somebody to do the upload (please use dch-r before...). But I have resumed my work on TS2, and I hope that I can send it to my application manager soon. Uploading right now. Thank you, Charles! Best

Re: Website broken

2007-10-12 Thread Nelson A. de Oliveira
Hi! On 10/12/07, David Paleino [EMAIL PROTECTED] wrote: Here's what happened: when Nelson committed the pt_* translations, he modified the permissions of the whole website. It has not been a conscious action, but a consequence of the post-commit hook. Mi scusi. Sorry for this trouble and

Re: Website broken

2007-10-12 Thread Nelson A. de Oliveira
On 10/12/07, David Paleino [EMAIL PROTECTED] wrote: I've added a umask 002 line to the update-website script. This *should* ensure the correct umask while updating the website. I'd need a test commit from someone who didn't set his umask yet (Nelson?). In any case, if this doesn't work (and

Re: New upload for proda

2007-09-30 Thread Nelson A. de Oliveira
Hi David! On 9/30/07, David Paleino [EMAIL PROTECTED] wrote: I think it's ready for an upload. ;) It is :-) Uploaded. Best regards, Nelson -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]

Re: New upload of emboss-explorer

2007-09-29 Thread Nelson A. de Oliveira
Hi David! Uploaded emboss-explorer. Thank you for your work! Best regards, Nelson -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]

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