Re: GBrowse2 packaging

[Olivier Sallou]

Hi,
I repackaged gbrowse2, I gonna update the svn of gbrowse on trunk

I will let you know once ready to have a look ...

Olivier

Le 2/6/11 1:52 PM, Charles Plessy a écrit :

Le Sun, Feb 06, 2011 at 10:49:42AM +0100, Olivier Sallou a écrit :

I am looking at GBrowse2 packaging.
If I succeed to do so, should I update the ITP you made on GBrowse ?

Feel free to document any progress or issue in the ITP, by CCing 
429...@bugs.debian.org

And to not hesitate to commit in the SVN without asking. Since I am subscribed
to the commit mailing list, it is the best way to submit a patch :)

Bon après-midi,



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Re: GBrowse2 packaging

[Olivier Sallou]

Hi,
gbrowse2 is packaged and SVN is updated in trunk.

There are quite many error/warnings with linthian due to the program files.

I wonder until which pach level I should go to make it available as I do 
not manage the sources...


I let you have a look and check this to upload the package.


Regards

Olivier

Le 2/23/11 2:36 PM, Olivier Sallou a écrit :

Hi,
I repackaged gbrowse2, I gonna update the svn of gbrowse on trunk

I will let you know once ready to have a look ...

Olivier

Le 2/6/11 1:52 PM, Charles Plessy a écrit :

Le Sun, Feb 06, 2011 at 10:49:42AM +0100, Olivier Sallou a écrit :

I am looking at GBrowse2 packaging.
If I succeed to do so, should I update the ITP you made on GBrowse ?
Feel free to document any progress or issue in the ITP, by CCing 
429...@bugs.debian.org


And to not hesitate to commit in the SVN without asking. Since I am 
subscribed

to the commit mailing list, it is the best way to submit a patch :)

Bon après-midi,





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gbrowse2 package

[Olivier Sallou]

Hi Charles,
will you have time to have a look to Gbrowse2 package or should I 
request an other sponsor ?


I successfully packaged it and removed most of lintian warns (a few man 
related remains)


Thanks

Olivier


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Re: gbrowse2 package

[Olivier Sallou]

I gonna have a look.
Most deps are set with perl debian package helper. I will try with pbuilder

Le 3/1/11 5:28 AM, Charles Plessy a écrit :

Le Tue, Mar 01, 2011 at 08:41:37AM +0900, Charles Plessy a écrit :

Le Mon, Feb 28, 2011 at 04:35:09PM +0100, Olivier Sallou a écrit :

Hi Charles,
will you have time to have a look to Gbrowse2 package or should I
request an other sponsor ?

I successfully packaged it and removed most of lintian warns (a few
man related remains)

Dear Olivier,

thanks a lot for all the work you did. I was super-busy this month, with
some family visit, and a very intensive conference at work. But I hope that
I will be able to look at Gbrowse2 this week.

Dear Olivier,

I had a very, very brief look and realised that gbrowse does not build in
a minimal environment (pbuilder, sbuild, …). Can you try to iterate through
the build dependancies and correct them? Here is the tail of the build log:

perl: already installed (5.10.1-17>= 5.10.0 is satisfied)
sqlite3: missing
libdbd-sqlite3-perl: missing
quilt: missing
libterm-readkey-perl: missing
Checking for dependency conflicts...
E: Broken packages
Installing positive dependencies: bioperl debhelper perl-depends 
libbio-graphics-perl libcapture-tiny-perl libcgi-session-perl 
libgd-gd2-noxpm-perl libio-string-perl libjson-perl 
libstatistics-descriptive-perl libwww-perl sqlite3 libdbd-sqlite3-perl quilt 
libterm-readkey-perl
Reading package lists...
Building dependency tree...
Reading state information...
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
  libbio-graphics-perl : Depends: libgd-gd2-perl (>= 2.3) but it is not going 
to be installed


Do not hesitate to ask for help or advice.

Also, I just read on the BioPerl mailing list that there may be an update soon.
This is probably very relevant for Gbrowse; let's keep an eye on it.

Have a nice day,



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Re: gbrowse2 package

[Olivier Sallou]

Hi Charles,
could you tell me which command you used ?

I tried with pbuilder:

pbuilder build gbrowse_2.26-1.dsc

and it works fine for me

Olivier

Le 3/1/11 5:28 AM, Charles Plessy a écrit :

Le Tue, Mar 01, 2011 at 08:41:37AM +0900, Charles Plessy a écrit :

Le Mon, Feb 28, 2011 at 04:35:09PM +0100, Olivier Sallou a écrit :

Hi Charles,
will you have time to have a look to Gbrowse2 package or should I
request an other sponsor ?

I successfully packaged it and removed most of lintian warns (a few
man related remains)

Dear Olivier,

thanks a lot for all the work you did. I was super-busy this month, with
some family visit, and a very intensive conference at work. But I hope that
I will be able to look at Gbrowse2 this week.

Dear Olivier,

I had a very, very brief look and realised that gbrowse does not build in
a minimal environment (pbuilder, sbuild, …). Can you try to iterate through
the build dependancies and correct them? Here is the tail of the build log:

perl: already installed (5.10.1-17>= 5.10.0 is satisfied)
sqlite3: missing
libdbd-sqlite3-perl: missing
quilt: missing
libterm-readkey-perl: missing
Checking for dependency conflicts...
E: Broken packages
Installing positive dependencies: bioperl debhelper perl-depends 
libbio-graphics-perl libcapture-tiny-perl libcgi-session-perl 
libgd-gd2-noxpm-perl libio-string-perl libjson-perl 
libstatistics-descriptive-perl libwww-perl sqlite3 libdbd-sqlite3-perl quilt 
libterm-readkey-perl
Reading package lists...
Building dependency tree...
Reading state information...
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
  libbio-graphics-perl : Depends: libgd-gd2-perl (>= 2.3) but it is not going 
to be installed


Do not hesitate to ask for help or advice.

Also, I just read on the BioPerl mailing list that there may be an update soon.
This is probably very relevant for Gbrowse; let's keep an eye on it.

Have a nice day,



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Re: gbrowse2 package

[Olivier Sallou]

Hi,
I gonna have a look for the -data package, but won't be so easy due to 
the way this is done in gbrowse


For other comments this is strange, I made some modifications to remove 
pl extensions errors, start/stop errors and INSTALL warning, I do not 
have lintian errors anymore on this...

When did you this?

Le 3/1/11 11:05 AM, Andreas Tille a écrit :

On Tue, Mar 01, 2011 at 05:13:36PM +0900, Charles Plessy wrote:

Le Tue, Mar 01, 2011 at 09:01:30AM +0100, Olivier Sallou a écrit :

Hi Charles,
could you tell me which command you used ?

I tried with pbuilder:

pbuilder build gbrowse_2.26-1.dsc

Hi Olivier,

I used sbuild…

I will not have time today, but I will also try with pbuilder later.

I used pbuilder the following way:

   $ sudo pbuilder update
   $ tar -xzf *.orig.tar.gz
   $ cp -a/debian GBrowse-2.26
   $ cd GBrowse-2.26
   $ pdebuild

This creates successfully a package where I have the following
issues:

   1. Scripts in /bin should be in /usr/bin and should not contain the
  *.pl extension (this was discussed several times on mailing lists -
  feel free to ask for more detailed reasons)
  Lintian:
  W: gbrowse: script-with-language-extension bin/bed2gff3.pl
  ...

   2. The only reason for an arch dependant package seems to be
   /usr/lib/perl5/auto/Bio/Graphics/Browser2/CAlign/CAlign.so
  It is not a good idea to have a package of large size (10MB) with
  only one single small file which is arch dependant.  So it is
  advisable to split this up in a reasonable manner.  I'd suggest
  to move /usr/share/gbrowse2/databases into a separate package
  gbrowse-data (arch=all).  This makes a sensible split and should
  be not to large in size for the arch=any part (remember:  All
  arch=any packages are ported to>10 architectures and mirrored
  to an order of at least 1000 mirrors world wide.  We should do
  our share to nowaste these resources.

   3. There is no need to provide a file
/usr/share/doc/gbrowse/INSTALL.gz
  Hey, tha package *is* installed, right?  If there are some things
  to do left, just mention it in README.Debian

   4. The init scripts do not support dependency based boot:

W: gbrowse: init.d-script-has-bad-start-runlevel /etc/init.d/gbrowse-slave 28
W: gbrowse: init-d-script-stops-in-s-runlevel /etc/init.d/gbrowse-slave
E: gbrowse: init.d-script-missing-dependency-on-remote_fs 
/etc/init.d/gbrowse-slave: required-start
E: gbrowse: init.d-script-missing-dependency-on-remote_fs 
/etc/init.d/gbrowse-slave: required-stop

   5. Some other important lintian issues:

E: gbrowse: package-installs-packlist usr/lib/perl5/auto/GBrowse/.packlist
W: gbrowse: package-contains-upstream-install-documentation 
usr/share/doc/gbrowse/INSTALL.gz
W: gbrowse: embedded-javascript-library 
usr/share/gbrowse2/htdocs/js/prototype.js
W: gbrowse: embedded-javascript-library 
usr/share/gbrowse2/htdocs/js/scriptaculous.js


Thanks for your work on this package and keep on asking if you need
help in one of the issues mentioned above

 Andreas.



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Re: gbrowse2 package

[Olivier Sallou]

I use latest lintian and man pages are present in my package, I checked.
Did you apply the patch?
I added many of the man pages with the patch

Lintian still show 3 missing man pages and some man issues in a few.
Fixing man issue may be difficult as doc is extracted from perl files 
automatically (perl2mod I think or something like that).


I gonna move bins as requested

Olivier

Le 3/1/11 3:40 PM, Andreas Tille a écrit :

On Tue, Mar 01, 2011 at 02:31:54PM +0100, Andreas Tille wrote:

Uhm, wait a moment - I had an old SVN checkout.  I'll keep on posting
later.

I commited two changes to SVN:

   1. Use wildcard when mentioning the manpages to install.
  This way dh_installmans does not try to install non-existing
  manpages (at least I can not find these in my tarball -
  there is only docs/gbrowse.1 but none of the others mentioned
  in your file.
  Any idea how to get the missing manpages?

   2. Move binaries from /bin to /usr/bin

Because you asked about lintian:  You most probably are using an
outdated lintian which is not as verbose as the one you get when trying

apt-get -t unstable install lintian

Please try again - there are other issues left and there are also hints
how to fix them whan using `lintian -i`.  Just ask again if even the
latest lintian does not produce any problem.

Kind regards

Andreas.




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Re: gbrowse2 package

[Olivier Sallou]

for javascript dependencies, gbrowse use the latest ones. I  can't 
consider using the debian ones as I do not know exact gbrowse 
requirements for those libraries. All I know is the current version in 
use as they include it.


One possible thing would be to upgrade prototype/scriptaculous to latest 
versions in debian repository.

Should I use maintainers to upgrade it?

Olivier


On Tue, Mar 01, 2011 at 03:51:52PM +0100, Olivier Sallou wrote:


>  I use latest lintian and man pages are present in my package, I checked.
>  Did you apply the patch?

Uhmm, not my day - old patch.:-(


>  I added many of the man pages with the patch

While it is perfectly valid to add the man pages via a patch (especially
if you plan to foreward this patch upstream) I would consider it way
more usual to move all manpages written by a Debian Maintainer to
debian/*.1.  So what you are doing is not really wrong but might not
be the best idea (= just a hint, feel free to keep it as is).



>  Lintian still show 3 missing man pages and some man issues in a few.
>  Fixing man issue may be difficult as doc is extracted from perl files
>  automatically (perl2mod I think or something like that).

If lintian is simply nitpicking and you would like to provide the
manpages that way you might consider debian/lintian-overrides to make
sure these warnings will not hide other problems.  With lintian 2.4.3
I get in addition to the manpage issues:

W: gbrowse: embedded-javascript-library 
usr/share/gbrowse2/htdocs/js/prototype.js
W: gbrowse: embedded-javascript-library 
usr/share/gbrowse2/htdocs/js/scriptaculous.js

As lintian suggests you might consider making the package dependant from
libjs-prototype and libjs-scriptaculous and add debian/links width

usr/share/javascript/prototype/prototype.js 
usr/share/gbrowse2/htdocs/js/prototype.js
usr/share/javascript/scriptaculous/scriptaculous.js 
usr/share/gbrowse2/htdocs/js/scriptaculous.js

(Just did something similar with python-cogent).



>  I gonna move bins as requested

I did it before I wrote my last mail.

Thanks for your packaging work (and sorry for the confusion I might have
caused when inspecting old code).  Charles, could your please have a
look if you consider it ready for sponsering?

Kind regards

Andreas.

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Re: gbrowse2 package

[Olivier Sallou]

It seems that main authors did not make such work :-( 
I will try to have a look for those files (css) or see with authors. 

Regarding included javascript librairies, expected versions are still in 
experimental. I contacted maintainer and he told me he should move them to sid 
in a short time. 

So i suggest to wait for those libraries to be moved to sid and I will update 
scripts to use them instead of packaging them with gbrowse. 
If this takes a too long time, I will keep them included for the moment... 

Olivier 

Le 3/7/11 2:09 AM, Charles Plessy a écrit : 

Le Tue, Mar 01, 2011 at 05:13:36PM +0900, Charles Plessy a écrit : 



I will not have time today, but I will also try with pbuilder later. 

Dear Olivier, 

I did not have time to try pbuilder. Instead, I inspected the source files of 
Gbrowse, and documented their copyright notices and licenses in 
debian/copyright. That was tedious and time-consuming, but it is required 
before uploading to the Debian archive. 

Default license is GPL version 1 or superior, or Artistic version 2. This 
license is not in /usr/share/doc/common-licenses, so it needs to be in 
debian/copyright. A large number of files are still GPL-1+ or Artistic (not 
version 2), and I grouped them in the same paragraph after collating their 
copyright notices. I also found some files whose license is MIT or LGPL. 

Importantly, I found files that are obviously not the work of the main authors, 
and that do not have a license. Of them, one is probably free (readseq.c), but 
for the other, htdocs/css/dropdown/default_theme.css and 
htdocs/css/dropdown/dropdown.css, there is not evidence that they are 
redistributable. We need the confirmation directly by the authors or through 
the Gbrowse developers. 

Can you or somebody else doublecheck that I have not forgotten something ? 

Have a nice day, 


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biomaj-watcher

[Olivier Sallou]

Hi Andreas, 
I have modified biomaj-watcher packaging to workaround packaging issues with 
dependencies. 


I still depend on GWT2 and a few other libs, but now I can compile all is 
required, so I do not hold anymore any biomajwatcher java class or lib 


All "binaries" are only external lib dependencies 


With this, biomaj-watcher should be candidate for non-free 


To do this I include in source required gwt libs etc... waiting for GWT2 to be 
packaged in sid (I tried to contact maintainers but I do not have any answer) 


I updated copyright file to set license for those dependencies. 


One point however, I try to use pbuilder to validate my package but 
biomaj-watcher depends on biomaj and it fails as biomaj is not found in 
packages (as not yet in official repository). How can I use pbuilder with 
pending packages ? 


Warning: you should update the source to test package as get-orig-source has 
been updated accordingly. 


Regards 


Olivier 

question on Tasks usage

[Olivier Sallou]

Hi,
could someone tell me how to install a debian-med task , such as bio-ngs 
etc...


Thanks

Olivier

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Re: question on Tasks usage

[Olivier Sallou]

Thanks for your answer.
In fact I do not have "urgent" need for ngs tasks, this was an example 
to understand behavior.


Classification is certainly not complete, but will never be I think.
Now we could define smaller categories (finer grain) but would be 
difficult to maintain (and difficult to place some packages which could 
be in several ones)


Regarding your previous email refered in this one, this is true that 
biology and med could be splitted in different blends (even tough some 
guys in medecin work with biology stuff in research departements), but 
this could
be misleading now with all existing references etc... on debian-med that 
would not be up-to-date anymore...


Maybe we could define a roadmap for this kind of classification that 
could be reviewed/updated on regular basis  upon users/developpers 
requests ?


Olivier



Le 3/15/11 5:16 PM, Andreas Tille a écrit :

as well as bio-phylogeny) I'm
hesitating a bit.  I created the NGS task in Travemünde and started a
discussion about it at [1].  In a similar manner I added the Phylogeny
task later when I visited a workshop here in m


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Bug#618689: ITP: squizz bioinformatics sequence converter tool

[Olivier Sallou]

Package: wnpp
Severity: wishlist
X-Debbugs-CC: debian-med@lists.debian.org

Maintainer: Olivier Sallou 
Language: C
License: GNU v2

Upstream Author: Nicolas Joly 
Homepage: ftp://ftp.pasteur.fr/pub/gensoft/projects/squizz/

Description:
Squizz is a sequence/alignment format checker, but it has some
conversion capabilities too.
Most common sequence and alignment formats are supported :
- EMBL, FASTA, GCG, GDE, GENBANK, IG, NBRF, PIR (codata), RAW, and
  SWISSPROT.
- CLUSTAL, FASTA, MEGA, MSF, NEXUS, PHYLIP (interleaved and sequential) and
  STOCKHOLM.

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Re: Bug#618689: ITP: squizz bioinformatics sequence converter tool

[Olivier Sallou]

Hi,
squizz is packaged on SVN and has been tested in my config (and pbuilder 
too).


Can someone check it and upload it, if ok ;-)

Thanks

Olivier

Le 3/17/11 8:47 PM, Andreas Tille a écrit :

Hi Olivier,

thanks for keeping us informed - tasks page will be updated after
next cron run

Andreas.

On Thu, Mar 17, 2011 at 05:56:23PM +0100, Olivier Sallou wrote:

Package: wnpp
Severity: wishlist
X-Debbugs-CC: debian-med@lists.debian.org

Maintainer: Olivier Sallou
Language: C
License: GNU v2

Upstream Author: Nicolas Joly
Homepage: ftp://ftp.pasteur.fr/pub/gensoft/projects/squizz/

Description:
Squizz is a sequence/alignment format checker, but it has some
conversion capabilities too.
Most common sequence and alignment formats are supported :
- EMBL, FASTA, GCG, GDE, GENBANK, IG, NBRF, PIR (codata), RAW, and
   SWISSPROT.
- CLUSTAL, FASTA, MEGA, MSF, NEXUS, PHYLIP (interleaved and sequential) and
   STOCKHOLM.

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Re: Bug#618689: ITP: squizz bioinformatics sequence converter tool

[Olivier Sallou]

Hi Andreas,
I am splitting squizz in packages squizz (binary), libsquizz and 
libsquizz-dev as you proposed.


I have an "issue" though, the generated libs (libsquizz) by the tool are 
libbioseq and libbioali, not some libsquizz-bioseq kind.


This raise a Warn in lintian.

Should I change the "make" files to modify the libs name, or is it 
acceptable anyway...


I could also create (sub)binary packages with package name libbioseq and 
libbioali, but I don't think it is acceptable to use several packages 
names (not like squizz-xxx). My control file would have source package 
squizz and binary packages squizz, libbioali, libbioseq


Thanks for your opinion

Olivier

Le 3/18/11 1:45 PM, Andreas Tille a écrit :

Hi Olivier,

thanks for working on this package.  (I actually have the impression
that Travemünde triggered some kind of competition who might package the
highest number of new packages. ;-))

I had a look into the packaging and I think it might work this way but
the existence of the libs leaves some space for enhancement.  In
addition I just commited some slight changes where I replaced general
comments in the boiler template - no need to talk about this further
here.

The problem is that if a software provides libraries these should be
provided as libfoo + libfoo-dev package while the former contains the
*.so.* files and the latter *.a + *.h files.  The binary tool which is
finally called by the user should go to either foo-tools.deb or in your
case simply squizz.deb.  So this is the general rule which you can read
in detail in the Library Packaging Guide[1].

There might be reasons to not follow this guide but these reasons should
be documented.  The fact that you included *.a and *.h files in the
package are in my eyes a clear sign that it might make sense that users
build their own programs linked against this library which makes perfect
sense to provide a libsquizz-dev package (or even a libbioali-dev +
libbioseq-dev ... whatever makes sense).

If those -dev packages would make sense then you should also have
separate library packages accordingly.  So the decision depends from the
fact whether such a development infrastructure should be provided or
not.  If it does not make sense the extra files should be left out of
the squizz packages (because we do not provide useless files).  If they
make sense we should (strongly) consider sticking to the suggested
package layout.

Kind regards and thanks for your work on squizz in any case

   Andreas.

On Fri, Mar 18, 2011 at 01:19:42PM +0100, Olivier Sallou wrote:

Hi,
squizz is packaged on SVN and has been tested in my config (and pbuilder
too).

Can someone check it and upload it, if ok ;-)

[1] http://www.netfort.gr.jp/~dancer/column/libpkg-guide/libpkg-guide.html



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Re: Bug#618689: ITP: squizz bioinformatics sequence converter tool

[Olivier Sallou]

Hi Charles,
I have a question regarding your work:

1) How did you find license issues ? (manual parse of all files?)

2) Regarding symbol file, how did you generate it ? (could help for 
further work)


Thanks

Olivier

Le 3/19/11 7:39 AM, Charles Plessy a écrit :

Le Fri, Mar 18, 2011 at 06:32:05PM +0100, Olivier Sallou a écrit :

I could also create (sub)binary packages with package name libbioseq
and libbioali, but I don't think it is acceptable to use several
packages names (not like squizz-xxx). My control file would have
source package squizz and binary packages squizz, libbioali,
libbioseq

Hi Olivier,

I think that as long as no other package depend on the bioali and bioseq
libraries, the current situation is sufficient.

I had a look and added a symbols so that the dependancy on libsquizz goes
through the shlibs:Depends substitution variable.

Unfortunately, I also found a non-free file. I think that our archive
administrators enforce the same policy for software code and for data.
Therefore, you have the choice between:

  - Delete the non-free file and disable the regression test(s) where
it is used.

  - Upload the package to the non-free section of the Debian archive,
instead of Debian proper.

  - Discuss with Upstream so that he finds a free replacement.

By the way, perhaps you can also report Upstream that the man pages that he
installs in the man5 directory still have ‘1’ as a section in their .TH line.
Correcting this would simplify their installation. Also, I see that you wrote a
manpage for squizz, but there is one from upstream as well, that you might have
overlooked.

Have a nice week-end,



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Re: Bug#618689: ITP: squizz bioinformatics sequence converter tool

[Olivier Sallou]

Hi,
I have updated and patched squizz to remove licensed file (used for testing)
I have packages: squizz, libsquizz and libsquizz-dev. I kept libraries 
in a single package as it does not really make sense to separate them.


I just have an issue with my lintian override I cannot make work (W: 
libsquizz: package-name-doesnt-match-sonames libbioali0 libbioseq0)
My override is not taken into account. I tried many things but there is 
certainly something wrong with it If you have an idea on how I 
should define it ?


I tried:
libsquizz binary: package-name-doesnt-match-sonames
and
libsquizz binary: package-name-doesnt-match-sonames libbioali0 libbioseq0

I also tried with source...

Thanks

Olivier



Le 3/18/11 8:40 PM, Andreas Tille a écrit :

On Fri, Mar 18, 2011 at 06:32:05PM +0100, Olivier Sallou wrote:

Hi Andreas,
I am splitting squizz in packages squizz (binary), libsquizz and
libsquizz-dev as you proposed.

I have an "issue" though, the generated libs (libsquizz) by the tool are
libbioseq and libbioali, not some libsquizz-bioseq kind.

This raise a Warn in lintian.

Should I change the "make" files to modify the libs name, or is it
acceptable anyway...

Yes, I know about this warning.  That's why I shortly mentioned that you
might consider two library and two dev packages.  However, I would only
do this split is it makes sense from the *content* of the library, i.e.
if each single library would make sense in its own.  Otherwise you might
consider overriding the lintian warning and add a comment inside the
override file, why splitting makes no sense.


I could also create (sub)binary packages with package name libbioseq and
libbioali, but I don't think it is acceptable to use several packages
names (not like squizz-xxx). My control file would have source package
squizz and binary packages squizz, libbioali, libbioseq

That's no question of name but rather a question of content.  There are
control files (try "apt-get source blast2" for example) which even
create different version numbers for some of the binary packages.  So
there is no need to bother about different naming.

Kind regards

  Andreas.



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Re: Bug#618689: ITP: squizz bioinformatics sequence converter tool

[Olivier Sallou]

This should be ok now.
I tested installed packages, man pages etc..

Copyright issue is fixed (at least worarounded).

Thanks for your help

Olivier

Le 3/21/11 12:32 PM, Andreas Tille a écrit :

On Mon, Mar 21, 2011 at 11:07:31AM +0100, Olivier Sallou wrote:

I just have an issue with my lintian override I cannot make work (W:
libsquizz: package-name-doesnt-match-sonames libbioali0 libbioseq0)
My override is not taken into account. I tried many things but there is
certainly something wrong with it If you have an idea on how I
should define it ?

I admit I had similar problems in the past and was not able to make out
any sense from it.  I had the feeling that if I install the package
containing th eoverride lintian is able to find the override file and is
able to regard it.  However, this methos was not always reliable.

I would decided to ignore this for the moment upload if no other
problems occure and fix it later (in case there is some need for fixing
any more).

Just keep us informed if this is the last issue and we should go on
with the upload.

Thanks for your work

   Andreas.



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Re: Bug#618689: ITP: squizz bioinformatics sequence converter tool

[Olivier Sallou]

ok , I gonna update to add a get-orig source to remove file and keep 
patch to remove tests on file.


I will let you know

Olivier

Le 3/21/11 1:44 PM, Andreas Tille a écrit :

On Mon, Mar 21, 2011 at 01:19:16PM +0100, Olivier Sallou wrote:

this is done in a patch debianpackaging, should it be stripped directly
via a get-orig-source?
I do not manage souce myself, I just do the packaging.

Sure.  But if the file in the source tarball is non-distributable
regarding DFSG we can not even put it in the source package (orig
tarball is part of this).  The source tarball is *distributed* by Debian
and this it makes the source non-free if it contains non-free files.

This is actually the sense why we use get-orig-source targets in some
cases.  The problem then should be documented in README.source to
express the fact that we do not ship a tarball which is identical to
what upstream provides at its site.


The watch file gets the orig tar from remote server and I added a patch
to remove file and relative tests.

This only prevents distribution in the binary package.

BTW, if I need to remove files from an original tarball I do the patches
to adapt the build system in the same step so the tarball which is
shipped via the Debian mirror is consistent and builds without problems
which might be caused by the removal of some files.  This is a personal
not documented habit of mine which IMHO just makes sense.

Kind regards

 Andreas.



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Re: Bug#618689: ITP: squizz bioinformatics sequence converter tool

[Olivier Sallou]

Hi,
I have created a get-orig-source that strips out the file, and a patch 
'debianpackaging' that updated the build related files to remove tests 
on the file.


Ran in "trunk", it creates a new orig.tar.gz in tarballs  (used other 
examples in svn)


Olivier

Le 3/21/11 1:15 PM, Andreas Tille a écrit :

On Mon, Mar 21, 2011 at 12:38:05PM +0100, Olivier Sallou wrote:

Copyright issue is fixed (at least worarounded).

I can not find code which strips the problematic file from the orig
source tarball.  This could be done in a get-orig-source target by
repackaging upstream tarball.  Or did I missed something?

Kind regards

Andreas.



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Re: Bug#618689: ITP: squizz bioinformatics sequence converter tool

[Olivier Sallou]

Thanks for your help at driving me for better/cleaner packaging

Olivier

Le 3/22/11 12:44 AM, Charles Plessy a écrit :

Le Mon, Mar 21, 2011 at 03:43:59PM +0100, Olivier Sallou a écrit :

I have created a get-orig-source that strips out the file, and a
patch 'debianpackaging' that updated the build related files to
remove tests on the file.

Dear Olivier,

thank you very much for all your efforts and your perseverance.

I have made a couple of extra modifications for the next release.  The
get-orig-sources script adds “.orig” to the source archive, in line
with Developers Reference 3.4.4 §6.7.8.2. I have also split the
debianpackaging patch into one for the manpages and one for disabling
the tests.  If you like, you can have a look to http://dep.debian.net/deps/dep3/
to further document them.

Have a nice day,



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gbrowse2 packaging

[Olivier Sallou]

Hi,
I have updated gbrowse packaging.

I fixed licensing issuess: dropdown css are GNU GPL (copyright updated) 
and I remove contrib directory from source via a get-orig-source target.

"Contribs" are not required for software.

Could you have a look at packaging for upload ?

Thanks

Olivier

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Re: gbrowse2 packaging

[Olivier Sallou]

I gonna move the man pages out of the page.

For the arch, there is a .so file generated in perl libs, that"s why it 
is dependent.


Regards

Olivier

Le 4/1/11 1:49 PM, Andreas Tille a écrit :

Hi Olivier,

On Fri, Apr 01, 2011 at 12:00:56PM +0200, Olivier Sallou wrote:

Could you have a look at packaging for upload ?

I had only a *very* quick look.  One thing I noticed is that you created
the manpage inside a patch.

--- /dev/null
+++ b/docs/gbrowse.1
...

I'd consider it better to move it as plain file in debian/gbrowse.1.

My change I did on debian/watch in SVN seems to be in fact unneeded - I
was just missleaded by a strange warning/error message but later realised
that the orig.tar.gz was actually created.  But it is fine to leave it
as it is now.

As I said I had only a very quick look, but it seems that the package
could perfectly be arch=all or did I miss some binary chunks of code
inside the package?

Any volunteer to finally test this package - I personally have no use
for this and having a web-service tested before upload seems to be
reasonable.

Kind regards and thanks for your work

Andreas.



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Re: gbrowse2 packaging

[Olivier Sallou]

Hi,
I splitted the package to remove the binary dependency. After some 
investigation, it appears that the CAlign stuff is not a requirement, 
but rather a "plugin" lib to provide additional performance in specific 
usages.


So, I created gbrowse package in arch=all, and gbrowse-calign in 
arch=any. gbrowse-calign is a Suggests (with gbrowse-data)


This should solve the size issue for arch.

Regards

Olivier


Le 4/1/11 2:54 PM, Andreas Tille a écrit :

On Fri, Apr 01, 2011 at 02:07:50PM +0200, Olivier Sallou wrote:

I gonna move the man pages out of the page.

OK.


For the arch, there is a .so file generated in perl libs, that"s why it
is dependent.

Ahh, I missed that piece.  From the size of the whole deb compared to
the size of the .so file it might make sense to split the arch=any and
the arch=all part into gbrowse_*_.deb and a
gbrowse-common_*_all.deb making gbrowse "Depends: gbrowse-common". I do
not have a strong opinion on this and there are always arguments against
such a split.  But the relation of a 2.5MB arch dependant Debian package
(which is copied for>  10 architectures over>  1000 mirrors all over the
world) because of a 12.5kB binary chunk inside does not sound good and
thus *I* would try to find a reasonable cut (while I did not thought
about what in this case is actually reasonable).  It might or might not
make sense to move all *.pm files and /usr/share/gbrowse to such a
common package.

So just take this as something to think about - I would definitely
sponsor the package if you decide to leave it as it is.

BTW, the "long" description of gbrowse-data is a bit short.  Moreover I
wonder if "Depends: gbrowse" is actually correct.  While you are
implying that this package does not make any sense if gbrowse is not
installed there might be users who would like to test those data with a
locally installed gbrowse (not from the Debian packaged version and thus
get even some conflict with their installation) or just want to use this
data for any other purpose.  I would only go for a Recommends in this
case to enable users installing data without beeing forced to have
gbrowse installed.

Kind regards

 Andreas.




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Re: gbrowse2 packaging

[Olivier Sallou]

The "default" web page access is given in man page. But I can add it in 
README.


Regarding all links available in "index" page, they provide access to 
many links, but those depends in fact on the install you made (


GBrowse provides many different possible installation types)

You can install as a basic cgi, but also use fastcgi etc... This is only a 
matter of install.

For packaging, I selected an install type , the one with access to 
"http://localhost/cgi-bin/gbrowse";


Maybe the easier would be to give this url as entry point (rather than example 
page), this would avoid misleading the user.


Regarding renderfarm, I need to have a look, it may be ok (or not...)


I gonna have a look and will let you know

Olivier


Le 4/1/11 6:25 PM, Andreas Tille a écrit :

uld solve the size issue for arch.

This looks much better!

Now for the final polishing.  I consulted README.Debian and I think it
needs more expertise than a normal user has to learn what to do next.
I as admin with experience assumed that I will have a clue once I have
a look into /etc/apache2/config.d/gbrowse to what URL I should point
my browser - but a kind explanation right inside README.Debian would
be definitely helpful.


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Re: gbrowse2 packaging

[Olivier Sallou]

Hi,
I have fixed gbrowse to:
1) fix the renderfarm issue found by Andreas (was due to a recent change in bin 
location)
2) removed the registration question from package build to remove interaction
3) updated README.source for additional info

One question Charles, in the version rename you made, you rename with ~dfsg , 
what is the meaning of dfsg?

That's all for me for the moment.

Thanks

Olivier

- Mail original -
> De: "Charles Plessy" 
> À: "Olivier Sallou" 
> Cc: "Debian Med Project List" 
> Envoyé: Samedi 2 Avril 2011 05:16:10
> Objet: Re: gbrowse2 packaging
> Le Fri, Apr 01, 2011 at 12:00:56PM +0200, Olivier Sallou a écrit :
> >
> > I have updated gbrowse packaging.
> >
> > I fixed licensing issuess: dropdown css are GNU GPL (copyright
> > updated) and I remove contrib directory from source via a
> > get-orig-source target.
> > "Contribs" are not required for software.
> >
> > Could you have a look at packaging for upload ?
> 
> Hi Olivier,
> 
> I only had time for cosmetic changes, but I notice that when running
> svn-buildpackage, I am asked a question about registration. This will
> cause
> problems, as building must be doable non-interactively and without
> internet
> access, so that the packages can be auto-build for other architectures
> on our
> trusted network.
> 
> Bon week-end !
> 
> --
> Charles


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gbrowse: auto tests added

[Olivier Sallou]

Hi, 
as requested by Charles, I added auto test step to rules file . 


Tests are run in non-interactive way. 


Olivier 

Re: Report from Med@Tel

[Olivier Sallou]

Hi,
regarding Twitter, it is very network related, you register to a feed and 
possibly forward to your followers. I am not sure this would finally 
"touch/ping" the final user. Either you already know Debian(Med), and this 
could be usefull as simple informational feed, or you don't know it and I am 
not sure Twitter will help...

Olivier

- Mail original -
> De: "Andreas Tille" 
> À: "Debian Med Project List" 
> Cc: "Debian Project" , "Debian Events EU" 
> 
> Envoyé: Dimanche 10 Avril 2011 19:43:14
> Objet: Report from Med@Tel
> Hi,
> 
> I would like to give a short report about my presence at Med@Tel in
> Luxembourg. This conference for medicine informatics had some Open
> Source track and the organisers invited me to give an introduction
> about
> Debian Med. The slides of my talk are available as well as the paper I
> submitted for the abstract book[1]. The audience were about 20 people
> somehow connected to some medical Open Source project and the talk was
> well received. (For instance I've got a warm handshake: "Thanks for
> what you are doing" afterwards.)
> 
> What always astonishes me is that people in all circumstances I'm
> reporting about Debian Med immediately agree with me that this is
> something which is really helpful and needed. However, even if I'm
> traveling through the world since eight years to talk about this
> concept
> - not only for the topic of medicine, also for other fields - people
> consider it brand new and they were not aware that such a thing really
> exists. The obvious conclusion is that I (or rather we Debian people)
> somehow failed in advertising it.
> 
> We could even say that Debian could serve as (buzz-word alarm)
> application store for different fields of work. While we probably are
> a
> bit nervous about such kind of buzz words it actually fits to some
> extend to what we are doing (at least I came to this conclusion when
> talking to other conference participants). More advertising adictive
> people than we would sell Debian as this. While I'm hesitating to sell
> Debian as "something" we probably need to adapt to the language our
> potential users are speaking to let them understand what we are doing.
> In times where importand people pronounce "Debian was a pointless
> exercise"[2] we should not trust that users simply find their way to
> Debian just by evaluating its technical brilliance. We (at least the
> Debian Med team) are now targeting at other user groups as well.
> 
> For instance I talked to an engaged Fedora user who liked the support
> of
> medical software inside Debian. When I told him that there is also
> support for Education, Science, Multimedia, GIS, Games, etc. he could
> not even believe this. (I think I finally got this guy convinced when
> I
> explained him that we even support kFreeBSD which enables him to use
> ZFS
> and it took me about 5min to make sure he really understood what we
> provide - at first he believed in certain hacks, chroots, VMs
> whatever.)
> 
> But this guy made an important point: If we obviosely fail in
> advertising the cool stuff we just have, what about using social media
> like Twitter, Facebook or LinkedIn. I'm personally quite ignorant of
> all this stuff. However, if I look over the shoulder of some of my
> friends and see with what pieces of "information" they are poluting
> the
> "byte space" by using twitter so that I'm convinced that it is a
> reasonable thing to ignore this medium - I could perfectly imagine to
> twitter any uploaded Debian package. Something like
> 
> Uploaded   - 
> 
> and in the case of Debian Med enriched with '#DebianMed' could do a
> reasonable job. Once implemented this could serve as a quite cheap way
> to get some attention amongst potential users.
> 
> What do you think about this and what other chances do you see to make
> use of social media to make the things we are doing right more
> popular?
> 
> Kind regards
> 
> Andreas.
> 
> 
> [1] http://people.debian.org/~tille/talks/201104_luxembourg
> [2]
> http://www.omgubuntu.co.uk/2011/01/our-exclusive-interview-with-linus-torvalds-lca2011/
> 
> --
> http://fam-tille.de
> 
> 
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Re: Uploading GBrowse to experimental ?

[Olivier Sallou]

Hi Charles,
the script metadb is used for the "user management". It creates a new 
"database" (sqlite) if not already created. It is required for some actions 
enabled by default at install.

I think we can remove it from post-install however. User can still execute it 
if required.

Olivier

- Mail original -
> De: "Charles Plessy" 
> À: "Olivier Sallou" , debian-med@lists.debian.org
> Envoyé: Dimanche 10 Avril 2011 13:28:04
> Objet: Uploading GBrowse to experimental ?
> Dear Olivier,
> 
> as you probably have seen on the commit mailing list, I have made a
> couple of
> changes to the gbrowse package. The goal of many of them was to make
> the build
> process more simple according to the common practices in Debian. I
> hope that
> you are not offended that I undid some of your work, just to redo it
> “our way”.
> I think that it will help other members of the Debian Med team to
> contribute.
> 
> My main problem is the postinst script that calls
> /usr/bin/gbrowse_metadb_config, as I do not understand well that this
> script is
> doing exactly. It looks like it creates and deletes directories under
> /usr and
> /var. I think that it is difficult to justify, as these directories
> may belong
> to the package itself. Indeed, gbrowse fails to be installed twice in
> a row
> when this script is enabled. Since it does not look necessary to at
> least run
> the examples, I disabled it for the moment. Similarly, GBrowse seems
> to create
> some files or directory under /usr at run time. This is also something
> that
> we will have to correct.
> 
> This said, I do not want to postpone the upload of the package ad
> vitam aeternam.
> How about uploading it to the experimental section of our archive ?
> Then we
> can keep on working on the issues above, and the proper setup of the
> render farm.
> 
> In the past, Upstream has been very suppportive and if we have GBrowse
> in
> experimental, I think that they will be very motivated to help us by
> adding
> some flexibility in GBrowse where needed.
> 
> Have a nice day,
> 
> --
> Charles Plessy
> Debian Med packaging team,
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan


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Re: Uploading GBrowse to experimental ?

[Olivier Sallou]

I will have a look for db location, I will certainly have to patch the code to 
move it.

Olivier

- Mail original -
> De: "Andreas Tille" 
> À: debian-med@lists.debian.org
> Envoyé: Lundi 11 Avril 2011 10:01:56
> Objet: Re: Uploading GBrowse to experimental ?
> On Mon, Apr 11, 2011 at 09:33:24AM +0200, Olivier Sallou wrote:
> > Hi Charles,
> > the script metadb is used for the "user management". It creates a
> > new "database" (sqlite) if not already created. It is required for
> > some actions enabled by default at install.
> >
> > I think we can remove it from post-install however. User can still
> > execute it if required.
> 
> IMHO the more urgent problem was *where* this database is created. It
> must not be created under /usr but rather in /var/lib/gbrowse. Could
> you please clarify this issue?
> 
> Kind regards
> 
> Andreas.
> 
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> 
> 
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Re: Uploading GBrowse to experimental ?

[Olivier Sallou]

Hi,
I have updated gbrowse to move "db" related data to /var/lib instead of 
/usr/share
I removed call to metadb_config script and updated config to disable 
user management by default (in fact I think it is best for default install).


I made a few updates too for the gbrowse_slave where a restart is 
required at gbrowse-data install.


To test it, please reload patches as I updated them.

Olivier

Le 4/11/11 9:33 AM, Olivier Sallou a écrit :

Hi Charles,
the script metadb is used for the "user management". It creates a new 
"database" (sqlite) if not already created. It is required for some actions enabled by 
default at install.

I think we can remove it from post-install however. User can still execute it 
if required.

Olivier

- Mail original -----

De: "Charles Plessy"
À: "Olivier Sallou", debian-med@lists.debian.org
Envoyé: Dimanche 10 Avril 2011 13:28:04
Objet: Uploading GBrowse to experimental ?
Dear Olivier,

as you probably have seen on the commit mailing list, I have made a
couple of
changes to the gbrowse package. The goal of many of them was to make
the build
process more simple according to the common practices in Debian. I
hope that
you are not offended that I undid some of your work, just to redo it
“our way”.
I think that it will help other members of the Debian Med team to
contribute.

My main problem is the postinst script that calls
/usr/bin/gbrowse_metadb_config, as I do not understand well that this
script is
doing exactly. It looks like it creates and deletes directories under
/usr and
/var. I think that it is difficult to justify, as these directories
may belong
to the package itself. Indeed, gbrowse fails to be installed twice in
a row
when this script is enabled. Since it does not look necessary to at
least run
the examples, I disabled it for the moment. Similarly, GBrowse seems
to create
some files or directory under /usr at run time. This is also something
that
we will have to correct.

This said, I do not want to postpone the upload of the package ad
vitam aeternam.
How about uploading it to the experimental section of our archive ?
Then we
can keep on working on the issues above, and the proper setup of the
render farm.

In the past, Upstream has been very suppportive and if we have GBrowse
in
experimental, I think that they will be very motivated to help us by
adding
some flexibility in GBrowse where needed.

Have a nice day,

--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan




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Re: Uploading GBrowse to experimental ?

[Olivier Sallou]

Hi,
what do you mean by :

And, it may be time for your Debian Maintainer application ?


Olivier

Le 4/12/11 5:09 PM, Steffen Möller a écrit :

Hello,

On 04/12/2011 04:20 PM, Charles Plessy wrote:

Le Tue, Apr 12, 2011 at 02:22:50PM +0200, Olivier Sallou a écrit :

I have updated gbrowse to move "db" related data to /var/lib instead
of /usr/share
I removed call to metadb_config script and updated config to disable
user management by default (in fact I think it is best for default
install).

I made a few updates too for the gbrowse_slave where a restart is
required at gbrowse-data install.

To test it, please reload patches as I updated them.

it works !

whow! many thanks.

During the next weeks I will be less available.  I will try to upload to
experimental tomorrow.  In addition to the package polishing, the next step
will go through a new upstream release of BioPerl.  If you are interested,
do not hesitate to:

debcheckout -a bioperl

and enjoy playing with Git !

Andreas has done many uploads over the past days ... many thanks.
I am a bit overbooked these days but uploads I can do, just  ping me.
And, it may be time for your Debian Maintainer application.

Steffen




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Debian Maintainer application vs DebianMed

[Olivier Sallou]

How does it work with DebianMed when applying for being Debian Maintainer ?
Packages are uploaded with the maintainer id "Debian Med Packaging Team".

Once we are an official Debian Maintainer, how can we manage updates on 
DebianMed packages as our id doest not appear as a maintainer. Is a 
special tag added somewhere ? Is it possible to become a maintainer of a 
package we were not first uploaders?


Thanks for the info.

Olivier

Le 4/13/11 9:32 AM, Andreas Tille a écrit :

On Wed, Apr 13, 2011 at 08:31:49AM +0200, Olivier Sallou wrote:

Hi,
what do you mean by :

And, it may be time for your Debian Maintainer application ?

What about Google: Debian Maintainer application ? :-)

It just simplifies things if you can upload packages yourself if you are
a Debian Maintainer.

Kind regards

  Andreas.



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Fwd: DM application of Olivier Sallou

[Olivier Sallou]

Hi,
I have sent a request to debian-newmaint list to become a Debian 
maintainer (see attached).

could you advocate me to support my application?

Thanks

Olivier

 Message original 
Sujet:  DM application of Olivier Sallou
Date :  Wed, 13 Apr 2011 14:38:01 +0200
De :Olivier Sallou 
Pour :  debian-newma...@lists.debian.org



This is my declaration of intent to become a Debian Maintainer
http://wiki.debian.org/DebianMaintainer>.
I have read the Social Contract, Debian Free Software Guidelines and
Debian Machine Usage Policy and agree with all of them.
Currently, I maintain the packages biomaj and squizz
and I co‐maintain the package gbrowse.
My GnuPG key 4096R/326D8438 is signed by the Debian Developers Steffen
Möller and Andreas Tille.
I look forward to becoming a Debian Maintainer. Thanks for your attention.

Olivier

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DM application of Olivier Sallou

[Olivier Sallou]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Hi,
I resent my application because my previous mail was not signed, as
expected.

This is my declaration of intent to become a Debian Maintainer
http://wiki.debian.org/DebianMaintainer>.
I have read the Social Contract, Debian Free Software Guidelines and
Debian Machine Usage Policy and agree with all of them.
Currently, I maintain the packages biomaj and squizz
and I co?maintain the package gbrowse.
My GnuPG key 4096R/326D8438 is signed by the Debian Developers Steffen
Möller and Andreas Tille.
I look forward to becoming a Debian Maintainer. Thanks for your
attention.

Olivier

- -- 
gpg key id: 4096R/326D8438  (pgp.mit.edu)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.9 (Darwin)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
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=0Q1s
-END PGP SIGNATURE-


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Re: Help from users needed (Was: Twitter and Social networks)

[Olivier Sallou]

I see there is a  Facebook page , but only with a description of the
project, did you created it?
In Facebook, you can fill events related to project (as Debian page), it
could be filled with events or general info

Not sure however, that info should be the same as on Twitter (do you
plan to post uploaded packages?)

Olivier

Le 4/14/11 3:40 PM, vane...@gmail.com a écrit :
> p twitter and identica accounts for Debian Med, later on the day
> I'll add a nice avatar, and later on the week I'll look how to post
> automatically and stuff.

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package status in page http://debian-med.debian.net/tasks

[Olivier Sallou]

Hi,
packages squizz and biomaj have been put in sid. This is not up-to-date
in debian-med tasks page.

I do not know if it is automatically updated via scripts or need manual
change.

Thanks

Olivier

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help wth tomcat 6.0.32

[Olivier Sallou]

Hi,
is anyone using tomcat 6.0.32 (current one on sid) ?

I have an issue where my webapp context file in
Catalina/localhost/myapp.xml is not taken into account.
Only WEB-INF/web.xml context is used (though should be overriden by the
previous).

This used to work long time ago (and works on other installs/distrib
with older tomcat).

Result is my package install test fails now...  :-(

I saw on google what looks like to be an issue on this (up to 0.32), but
I am not 100% sure.

If someone has such app using Catalina/localhost context would help me
to see if it is a Tomcat issue, or something on my side with my packaging.

Thanks

Olivier

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Re: Biomaj: location of pid file

[Olivier Sallou]

Hi, 
this is indeed a bug. It is no blocking but I will give a patch new week. 
We will remove it from shell script I think to create the pid file directly in 
the program using conf data. 
This pid file is just used to prevent dual updates on same banks. 


Would you mind create a bug under biomaj package for this (reportbug)? (I have 
intermittent access to internet this week). If you can't i will create it next 
week 


Thanks 


Olivier 




Helo, 
I installed and tried Biomaj, thanks for your job Olivier, 
No problem during install and running th 
e sample alu db. 
But, I got an minor error 

/usr/share/biomaj/bin/biomaj.sh: line 103: / usr/share/biomaj/tmp / 
.bmajpid_alu: Aucun fichier ou dossier de ce type (for no french speaker => 
means no found or directory found) 

In fact /usr/share/biomaj/tmp doesn't exist, and I think is ok with the debian 
policy. 
The code in biomaj.sh is : 

echo $$>$BIOMAJ_ROOT/tmp/.bmajpid_$arg 

with $BIOMAJ_ROOT = /usr/share/biomaj 

There is a tmp directory for biomaj (tmp.dir in /etc/biomaj/general.conf) but 
it's use by the java code not the shell script starting biomaj. 

I think that the pid file should go to /var/lib/biomaj/tmp or /var/run/biomaj 
or either /tmp 
/var/lib/biomaj/tmp is created by the package so it can be use, even if you 
change the location in general.conf (like I did, to put databases on another 
partition). 

But, I don't know the solution to correct this error. 


Thanks again for the packaging. 

Best regard, 
Anthony. 



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Re: Help with maven based package needed (dcm4che)

[Olivier Sallou]

In the maven Jar creation step, a Manifest description should be present. Maybe 
it refers a Manifest file instead of specifying its contents dynamically. 
Either Manifest file is not present at all, or it is in src but not copied in 
target dir (compilation copies only java classes, not other files). 
Olivier 
Hi,

I have a question to the next Java package for the Debian Med Blend.
The preliminary packaging stuff is available at

   svn://svn.debian.org/svn/debian-med/trunk/packages/dcm4che/trunk

The rules file is featuring a get-orig-source target so you can easily
obtain the source tarball.  The build is running into the following
error:

...
[INFO] [jar:jar {execution: default-jar}]
[INFO] 
[ERROR] BUILD ERROR
[INFO] 
[INFO] Error assembling JAR

Embedded error: Manifest file: 
/tmp/buildd/dcm4che-2.0.25/dcm4che-audit/target/classes/META-INF/MANIFEST.MF 
does not exist.
[INFO] 
[INFO] For more information, run Maven with the -e switch
...


Any idea what might be wrong here?

Kind regards

   Andreas. 
-- http://fam-tille.de 

Re: Help with maven based package needed (dcm4che)

[Olivier Sallou]

Hi,
pom should be patched I think to specify yourself the Manifest data.
Unfortunatly, this week I am not at home/work, I can't have a look 
(intermittent internet access).

I can have a look next week if you want.

Olivier

- Mail original -
> De: "Andreas Tille" 
> À: "Debian Med Project List" 
> Cc: "Debian Java List" 
> Envoyé: Mardi 19 Avril 2011 18:12:28
> Objet: Re: Help with maven based package needed (dcm4che)
> Hi Olivier,
> 
> On Tue, Apr 19, 2011 at 06:00:16PM +0200, Olivier Sallou wrote:
> > In the maven Jar creation step, a Manifest description should be
> > present. Maybe it refers a Manifest file instead of specifying its
> > contents dynamically. Either Manifest file is not present at all, or
> > it is in src but not copied in target dir (compilation copies only
> > java classes, not other files).
> 
> Your analysis makes sense because I at first created the packaging
> stuff
> using maven_helper. Afterwards I fetched an independent source archive
> via uscan which was not prepared with maven_helper and thus might be
> missing those files.
> 
> But what will be the solution for this problem? I'd consider the uscan
> method to get the source as "my prefered way to go". Is it possible to
> tweak this Manifest file in via a quilt patch somehow?
> 
> Kind regards
> 
> Andreas.
> 
> --
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> 
> 
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biomaj-watcher

[Olivier Sallou]

Hi,
I have packaged biomaj-watcher, now that biomaj is in official repository.
(upstream source has been updated, it needs to be refreshed)

I tested with pbuilder and it looks fine.

It integrates some jar files as GWT2 is not packaged in Debian (and I am
not confident enough to do it now), as well as a few other open source
libraries that need GWT2 too.

As such, it should be uploaded to contrib or non-free (included binaries
are open source, it is only a matter of packaging), not sure exactly
which one.
When GWT2 is package, I should be able to remove binaries from package.

Thanks for having a look and uploading it if ok.

Regards

Olivier

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Re: Re: DM application of Olivier Sallou

[Olivier Sallou]

Hi,
I have update my key to add the E usage flag. I have uploaded it to gpg
servers (keys.gnupg.net)

Regards

Olivier

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Fwd: biomaj-watcher

[Olivier Sallou]

Hi,
just a new ping for biomaj-watcher, as I did not get any answer from my
previous post.
If someone can take it in charge for check/upload, please just inform me
(not urgent, but just so that I know that someone got it).

Thanks

Olivier

 Message original 
Sujet:  biomaj-watcher
Date de renvoi :Fri, 22 Apr 2011 11:47:03 + (UTC)
De (renvoi) :   debian-med@lists.debian.org
Date :  Fri, 22 Apr 2011 13:46:47 +0200
De :Olivier Sallou 
Pour :  Debian Med Project List 



Hi,
I have packaged biomaj-watcher, now that biomaj is in official repository.
(upstream source has been updated, it needs to be refreshed)

I tested with pbuilder and it looks fine.

It integrates some jar files as GWT2 is not packaged in Debian (and I am
not confident enough to do it now), as well as a few other open source
libraries that need GWT2 too.

As such, it should be uploaded to contrib or non-free (included binaries
are open source, it is only a matter of packaging), not sure exactly
which one.
When GWT2 is package, I should be able to remove binaries from package.

Thanks for having a look and uploading it if ok.

Regards

Olivier

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Re: biomaj-watcher

[Olivier Sallou]

see answer below

Le 4/26/11 11:42 AM, Andreas Tille a écrit :
> Hi Olivier,
>
> On Fri, Apr 22, 2011 at 01:46:47PM +0200, Olivier Sallou wrote:
>> Hi,
>> I have packaged biomaj-watcher, now that biomaj is in official repository.
>> (upstream source has been updated, it needs to be refreshed)
> You mean there is a new version of biomaj-watcher which is more up to
> date than the version fitting the current packaging?  If yes, I'd suggest
> to package the latest upstream version (if no strong reason is against
> this).
>
Olivier: no, biomaj is still the same, and latest code of biomaj-watcher
fits this version of biomaj. The upstream source of biomaj-watcher have
been updated to fit the current packaging (removal of some binary), so
in case you made a get-orig-source of biomaj-watcher some time ago, you
should re-run it to get the latest biomaj-watcher source.
>> I tested with pbuilder and it looks fine.
> I had a *very* quick look (did not yet builded the package) but I would
> be happy if you could try to make the description in the control file a
> bit more verbose.

Olivier: I will
>  
>> It integrates some jar files as GWT2 is not packaged in Debian (and I am
>> not confident enough to do it now), as well as a few other open source
>> libraries that need GWT2 too.
> Have you checked debian-java list whether there is some effort about this
> ongoing?
>  
> My time is a bit limited this week but I'll try to do my best to have a
> deeper look.
Olivier: I pinged some time ago the debian GWT maintainers, but got no
answer.
Thanks for your time...
> Kind regards
>
>Andreas.
>

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help wanted for first patch on my package

[Olivier Sallou]

Hi,
I have made my first patch for Biomaj, after it is uploaded in Debian repo.
Could someone please confirm, to help me doing the things correctly.

I have in Debian bugs 2 bug ids (1 bug, 1 wishlist).

I fixed the first with a new patch (quilt)
Second one impacts debian directory only (add a debconf translation), so
I added the new .po file in debian/po dir.
I update the Changelog to have a new release (xxx-1.1 after -1) and
declare Closed bugs.

Thanks

Olivier

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what to do if upgrade is not possible?

[Olivier Sallou]

Hi,
shame on me, I have an error in debian scripts of my package preventing
an upgrade of the package (install is ok).

While I fixed it in the new package (for further updates), in the
meanwhile it means that if an upgrade is needed, one must first
uninstall the package, then install the new one.

I'd like to know what is the best solution:

1) update preinst etc.. to detect that it is an upgrade from version X ,
and raise an error with explanatory message. User will have to do the
removal/install manually. Package cannot revert automatically to version
X, it will be broken. However user is safe from data/config point of view.

2) put in the new package a Conflicts with itself for the version X 
(Version Y conflicts with Version X).

Thanks

Olivier

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blast+ packaging

[Olivier Sallou]

Hi,
I see in tasks the ncbi Blast+ software, not packaged.

Has anyone started something? Or should I go for it ?

Olivier

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Re: blast+ packaging

[Olivier Sallou]

Hi,
thanks for the info.

Regarding binaries size vs compiled from source, I know that by default,
compilation is done with debug enabled, and
increase size/lower performance.

For uscan I did not have a look yet, for the moment I will try to get
compilation done...


The legacy_blast.pl is given in the source code. I will have a look at
alternatives when basic compile/install is ok.

Olivier


Le 4/27/11 4:32 PM, Tim Booth a écrit :
> Hi Olivier,
>
> This was on my RADAR but I'm currently about to tackle AmplicoNoise
> (must remember to file an ITP before I start...) so please go ahead.  I
> had a look at it at the sprint and this is what I found:
>
> 1) This may have been down to our rubbish wireless link but there
> appeared to be something stopping automated downloads (ie. Uscan) from
> NCBI.  I know they do have anti-leeching on some of their sites.  Do you
> get any problems?
>
> 2) The current blast2 package has a version that tallies with the blast+
> version - ie. 1:2.2.24.20100808-2, yet the blast2 package doesn't
> contain Blast+ and I can't see where this version is coming from in
> blast2 given that it is built from the NCBI C toolkit which is versioned
> by date.  I started to look into this and ran out of time - any idea?
>
> 3) There is a handy script called legacy_blast.pl that emulates blastall
> and thus allows BLAST+ to be used with tools like T-Coffee.  I can't
> remember if this is in the upstream tarball or not, but if so it might
> be worth using the alternatives system to allow BLAST+ to fill in for
> legacy BLAST.
>
> 4) The BLAST+ binaries, if downloaded pre-compiled from NCBI, come in at
> a whopping great size compared to the source code.  I was meaning to
> look into what was going on (muchos static linking??) but never got
> around to it.
>
> 5) There should be a default $BLASTDB directory, I think.  Can't
> remember what the Debian policy is on apps that need a certain
> environment set before they will run but I'm sure the basic idea is to
> try and set defaults so the app will run out-of-the-box.
>
> Anyway, I gather BLAST+ should be less of a beast to package then the
> original, so have fun.  I'm not very good at reading the list so if you
> are able to CC me on any messages that would be appreciated.
>
> Cheers,
>
> TIM
>
> On Wed, 2011-04-27 at 14:53 +0200, Andreas Tille wrote:
>> Hi Olivier,
>>
>> On Wed, Apr 27, 2011 at 02:35:55PM +0200, Olivier Sallou wrote:
>>> Has anyone started something? Or should I go for it ?
>> If you are brave enough to tackle this there are several people who
>> would be happy about this (and some other programs depend from it.
>>
>> I would strongly advise to CC Aaron Ucko (as I did now) because he is
>> the ncbi / blast expert and I think I remember he had given some
>> statement about blast+.  While Aaron is a member of the Debian Med team
>> he does not follow this list strictly - so CCing him makes sense.
>>
>> Kind regards
>>
>>Andreas.
>>
>> -- 
>> http://fam-tille.de
>>
>>

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Biomaj package new delivery for bug fixes

[Olivier Sallou]

Hi,
I have updated the Biomaj package to fix 2 bugs and 1 wishlist.
It impacts debian files and adds a patch.

Would you mind uploading it (I do not have yet the maintainer status)

Thanks

Olivier

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svn-buildpackage error help

[Olivier Sallou]

Hi,
I have an issue in my packaging build . If someone could help or give
some hints.

In my ncbi-blast-plus packaging, I can do a fakeroot debian/rules 
clean/binary.
Package is generated correctly.

When I go to my trunk dir, and execute

svn-buildpackage -rfakeroot -uc -us


my build fails with the following messages "dpkg-source: warning:
ignoring deletion of file", and indeed, in my build-area dir, files are
not present.
Though my file ncbi-blast-plus_2.2.25.orig.tar.bz2 contains the files.

Here is an extract of build:
dpkg-buildpackage -rfakeroot -uc -us
dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor):
-g -O2
dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin:
vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor):
-g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package ncbi-blast-plus
dpkg-buildpackage: source version 2.2.25-1
dpkg-buildpackage: source changed by Olivier Sallou 
dpkg-buildpackage: host architecture amd64
 dpkg-source --before-build ncbi-blast-plus-2.2.25
 fakeroot debian/rules clean
dh clean
   dh_testdir
   dh_auto_clean
   debian/rules override_dh_clean
make[1]: Entering directory
`/opt/DEBIAN-MED/trunk/packages/ncbi-blast-plus/build-area/ncbi-blast-plus-2.2.25'
dh_clean
find . -name ncbiconf_unix.h | xargs rm -f
make[1]: Leaving directory
`/opt/DEBIAN-MED/trunk/packages/ncbi-blast-plus/build-area/ncbi-blast-plus-2.2.25'
 dpkg-source -b ncbi-blast-plus-2.2.25
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: info: building ncbi-blast-plus using existing
./ncbi-blast-plus_2.2.25.orig.tar.bz2
dpkg-source: warning: ignoring deletion of file configure
dpkg-source: warning: ignoring deletion of file src/Makefile.in
dpkg-source: warning: ignoring deletion of directory src/corelib
dpkg-source: warning: ignoring deletion of file src/corelib/ncbitime.cpp
dpkg-source: warning: ignoring deletion of file
src/corelib/ncbi_os_mswin.cpp
dpkg-source: warning: ignoring deletion of file src/corelib/env_reg.cpp
dpkg-source: warning: ignoring deletion of file
src/corelib/plugin_manager.cpp
dpkg-source: warning: ignoring deletion of file src/corelib/ncbi_base64.c
dpkg-source: warning: ignoring deletion of file
src/corelib/ncbi_autoinit.cpp
...

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Re: svn-buildpackage error help

[Olivier Sallou]

gotcha!

I used existing dir in svn tree for ncbi-blast-plus, did not think that
all svn stuff was not set.

Thanks

Le 4/29/11 1:15 PM, Steffen Möller a écrit :
> Have you set
>
> svn propset mergeWithUpstream 1 debian
>
> ?
>
> Cheers,
>
> Steffen
>
> On 04/29/2011 11:28 AM, Olivier Sallou wrote:
>> Hi,
>> I have an issue in my packaging build . If someone could help or give
>> some hints.
>>
>> In my ncbi-blast-plus packaging, I can do a fakeroot debian/rules 
>> clean/binary.
>> Package is generated correctly.
>>
>> When I go to my trunk dir, and execute
>>
>> svn-buildpackage -rfakeroot -uc -us
>>
>>
>> my build fails with the following messages "dpkg-source: warning:
>> ignoring deletion of file", and indeed, in my build-area dir, files are
>> not present.
>> Though my file ncbi-blast-plus_2.2.25.orig.tar.bz2 contains the files.
>>
>> Here is an extract of build:
>> dpkg-buildpackage -rfakeroot -uc -us
>> dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor):
>> -g -O2
>> dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
>> dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin:
>> vendor): -g -O2
>> dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor):
>> -g -O2
>> dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
>> dpkg-buildpackage: source package ncbi-blast-plus
>> dpkg-buildpackage: source version 2.2.25-1
>> dpkg-buildpackage: source changed by Olivier Sallou 
>> dpkg-buildpackage: host architecture amd64
>>  dpkg-source --before-build ncbi-blast-plus-2.2.25
>>  fakeroot debian/rules clean
>> dh clean
>>dh_testdir
>>dh_auto_clean
>>debian/rules override_dh_clean
>> make[1]: Entering directory
>> `/opt/DEBIAN-MED/trunk/packages/ncbi-blast-plus/build-area/ncbi-blast-plus-2.2.25'
>> dh_clean
>> find . -name ncbiconf_unix.h | xargs rm -f
>> make[1]: Leaving directory
>> `/opt/DEBIAN-MED/trunk/packages/ncbi-blast-plus/build-area/ncbi-blast-plus-2.2.25'
>>  dpkg-source -b ncbi-blast-plus-2.2.25
>> dpkg-source: info: using source format `3.0 (quilt)'
>> dpkg-source: info: building ncbi-blast-plus using existing
>> ./ncbi-blast-plus_2.2.25.orig.tar.bz2
>> dpkg-source: warning: ignoring deletion of file configure
>> dpkg-source: warning: ignoring deletion of file src/Makefile.in
>> dpkg-source: warning: ignoring deletion of directory src/corelib
>> dpkg-source: warning: ignoring deletion of file src/corelib/ncbitime.cpp
>> dpkg-source: warning: ignoring deletion of file
>> src/corelib/ncbi_os_mswin.cpp
>> dpkg-source: warning: ignoring deletion of file src/corelib/env_reg.cpp
>> dpkg-source: warning: ignoring deletion of file
>> src/corelib/plugin_manager.cpp
>> dpkg-source: warning: ignoring deletion of file src/corelib/ncbi_base64.c
>> dpkg-source: warning: ignoring deletion of file
>> src/corelib/ncbi_autoinit.cpp
>> ...
>>
>

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blast+ packaging

[Olivier Sallou]

Hi,
I have a blast+ packaging that looks to work.

Would you mind having a look ? It is in svn at ncbi-blast-plus

I tested a sample blastn that worked.
I also patched the upstream for a build issue and gcc 4.6 build.


Thanks

Olivier

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Re: blast+ packaging

[Olivier Sallou]

Hi, 
thanks for your reviews. 
I won't have time to progress in next 2 weeks. 
I will refresh svn and have a look at this time 


For boost, I did not know what was exactly required, I just saw that it was 
required for compil. 


For zlib etc... included in code, I think we should keep the copies (even if 
not using them). Removing them may be complex 'cause it would also require 
makefile stuff updates... 
I'd like to be as close as possible form original source code for maintenance 


For additional package, do you mean an "identical" blast package with just 
binaries renamed. to avoid conflicts? to be used in place of "basic" package? 


Olivier 






Tim Booth  writes: 

> I'm having a look at the package now.  I've pushed some changes to SVN > 
> already - I hope you don't mind.  To explain... Thanks for getting the review 
> process started!  I'll give more feedback
once I've had time to take a closer look at the packaging, but in the
meantime here's my take on the points you've raised. 

> I don't think you need to repack the source in this case.  The > guidelines 
> say to rename the tarball file, but not to change the > contents unless there 
> is a pressing reason to do so.  I've tweaked the > rules file to work with 
> the pristine source. Indeed; while there's no need for the convenience copies 
> of zlib, bzlib, or
libpcre, their presence poses no legal complications, so it should suffice
to document them in debian/copyright.  For that matter, there's also no
need to spell out "-plus." 

> Do we really need all boost libs installed to build and run correctly? No, 
> libboost-test-dev should suffice, and even then only if you want to
build (and presumably run) the test suite.  I also see no need for build
dependencies or explicit runtime dependencies on shared libraries. 

> I don't think we can get away with having this package conflict with > 
> blast2. Right, coexistence would be better, and I like the renaming idea.  
> That
said, I would consider alternatives and diversions to be legitimate
possibilities as well; likewise for shipping an additional package that
just arranges by whatever means for rpsblast et al. to run BLAST+ binaries. 
-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) 
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu 

bmaj watcher packaging

[Olivier Sallou]

Hi Andreas, 
do you think you will have some time to check biomaj-watcher? 


Thanks 


Olivier 

biomaj-watcher needs sponsor

[Olivier Sallou]

Hi,
I need a sponsor to push biomaj-watcher to FTP master.

biomaj-watcher is the graphical front-end of Biomaj.


Andreas did the job for Biomaj but will lack of time for this one.

Thanks

Olivier

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Re: biomaj-watcher needs sponsor

[Olivier Sallou]

thanks

Andreas already had a look and I made several changes according to his
comments.
If you see others...


Olivier

Le 5/9/11 12:56 PM, Steffen Möller a écrit :
> Hi Olivier,
>
> On 05/09/2011 09:31 AM, Olivier Sallou wrote:
>> Hi,
>> I need a sponsor to push biomaj-watcher to FTP master.
>>
>> biomaj-watcher is the graphical front-end of Biomaj.
>>
>>
>> Andreas did the job for Biomaj but will lack of time for this one.
> I can go for it.
>
> Steffen
>
>

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Re: blast+ packaging

[Olivier Sallou]

Hi,
for info I could make a few changes ot blast+ packaging:

- rename package to ncbi-blast+ (instead of -plus).
- create a ncbi-blast+-legacy which adds some scripts for legacy blast
that calls the blasT_legacy perl script to keep available previous
command line (shell scripts in /usr/share/ncbi-blast+/bin)
- keep libboost-test only at build time.


Olivier

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Re: biomaj-watcher needs sponsor

[Olivier Sallou]

Hi,
just as a reminder, biomaj-watcher embeds some jar file due to the fact
that GWT2 is not packaged (I created a request ticket for this).
All included jars are open source (described in copyright).

So I do not know if package must be sent to contrib or non-free.

Regards

Olivier

Le 5/9/11 12:56 PM, Steffen Möller a écrit :
> Hi Olivier,
>
> On 05/09/2011 09:31 AM, Olivier Sallou wrote:
>> Hi,
>> I need a sponsor to push biomaj-watcher to FTP master.
>>
>> biomaj-watcher is the graphical front-end of Biomaj.
>>
>>
>> Andreas did the job for Biomaj but will lack of time for this one.
> I can go for it.
>
> Steffen
>
>

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Re: [sc...@scottcain.net: [Gmod-gbrowse] Switch from SourceForge svn to Github git repository]

[Olivier Sallou]

ok for me but this will have impact on get-orig-source.
and I am not familiar with the debian build commands with git, this will
be a way to train...

Olivier

Le 5/12/11 1:58 AM, Charles Plessy a écrit :
> om svn at SourceForge to git at GitHub.  While we expect
> the transition to fairly painless,

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gbrowse build on Ubuntu

[Olivier Sallou]

Hi,
I see that Gbrowse failed to build on Ubuntu.


The following packages have unmet dependencies:
 libhttp-daemon-perl : Depends: libhttp-message-perl but it is not going to be 
installed
   Depends: libhttp-date-perl but it is not going to be 
installed
   Depends: liblwp-mediatypes-perl but it is not going to 
be installed
   Breaks: libwww-perl (< 6.00) but 5.837-1 is to be 
installed

Though those packages appear in Ubuntu launchpad.
It may be due to date tests (build date between packages).

Do you know how builds are manage at Ubuntu ? e.g. when Gbrowse build
should be retried to check its status ?

Olivier

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Re: gbrowse build on Ubuntu

[Olivier Sallou]

it is on public one, with oneiric release (next one).

https://launchpad.net/ubuntu/+source/gbrowse/2.26~dfsg-3


It may be just a matter a sync between dependencies, but I do not know
how Ubuntu manage its builds.

Olivier

Le 5/12/11 10:12 AM, Charles Plessy a écrit :
> Le Thu, May 12, 2011 at 09:58:37AM +0200, Olivier Sallou a écrit :
>> I see that Gbrowse failed to build on Ubuntu.
>>
>> The following packages have unmet dependencies:
>>  libhttp-daemon-perl : Depends: libhttp-message-perl but it is not going to 
>> be installed
>>Depends: libhttp-date-perl but it is not going to be 
>> installed
>>Depends: liblwp-mediatypes-perl but it is not going 
>> to be installed
>>Breaks: libwww-perl (< 6.00) but 5.837-1 is to be 
>> installed
> Bonjour Olivier,
>
> is this a build on your computer, or a public one ?  In that case, do you have
> an URL in which we can get more information (which suite, are there backports
> enabled, …).
>
> Cheers,
>

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biomaj-watcher

[Olivier Sallou]

Hi Steffen,
I have a question regarding biomaj-watcher package.

The package references the same ITP than biomaj. As biomaj has already
been uploaded, ITP has been closed (per the Closes in changelog).

Should biomaj-watcher reference a new ITP or is it ok to keep the same
as biomaj and biomaj-watcher are closely linked.

Thanks

Olivier

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Re: blast+ packaging

[Olivier Sallou]

Hi,
did you had time to look at ncbi-blast+ package before pushing it ?

Thanks

Olivie

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Re: blast+ packaging

[Olivier Sallou]

Hi,
please feel free to commit in my dir. It will indeed be easier than merging.
Your deep knowledge of compilation stuff of blast is one of the reason I asked 
you to review the package.
I am sure that your updates will be perfect.

For dir updates, be it ncbi-blast+ or ncbi-blast-plus, I would rather like you 
update directly in my branch. We can, after that, "mv" the svn dir to 
ncbi-blast+ once everything is ok from packaging point of view.

Please tell me once you have included your updates so that I recheck the 
package on my side.

Regarding legacy, I prefered keeping it as separate package to avoid some 
confusion and get it only if required on backward compatibility. Though, if you 
think we should keep it in the same package, it is ok for me.

Thanks for your help

Olivier

- Mail original -
> De: "Aaron M. Ucko" 
> À: "Andreas Tille" 
> Cc: "Aaron M. Ucko" , "Olivier Sallou" 
> 
> Envoyé: Samedi 28 Mai 2011 18:06:35
> Objet: Re: blast+ packaging
> Andreas Tille  writes:
> 
> > [Olivier in CC]
> 
> Thanks; I had considered that myself.
> 
> > If you ask me this is no question of politeness. I personally would
> > prefer if somebody would commit straight to the place where I was
> > working and I would not need to do any fiddling around with SVN to
> > merge both. I'm just mentioning this - feel free to find a common
> > agreement with Olivier.
> 
> Once the changes are in the repository, anyone can readily merge them
> into .../ncbi-blast-plus if Olivier wants to keep that path. OTOH, if
> he's open to the path change, this is as good a way as any to
> establish it.
> 
> --
> Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
> http://www.mit.edu/~amu/ |
> http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu


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bmaj watcher packaging

[Olivier Sallou]

Hi, 
following your remarks, I am looking at adding binary dependencies source code. 


However, after a look, source dependency is quite huge (GWT/SmartGWT, others 
are fine). 


I wonder if I really need to add source code for those in my package, or if a 
reference to source code URL would be fine. 


Thanks 


Olivier 

Re: blast+ packaging

[Olivier Sallou]

Hi,
are you talking of blast or blast+ ?

Regarding features, I do not see what you mean by xalan feature, or uuid 
(sounds like java packages).

Olivier

- Mail original -
> De: "George Marselis" 
> À: "Debian Med Project List" 
> Envoyé: Dimanche 29 Mai 2011 13:57:28
> Objet: Re: blast+ packaging
> since we are on the subject, i have been trying to compile ncbi-blast
> on my own, for my own use. i would like to enable ever single one of
> it's features; eg, UUIDs . or xalan. I cannot find any info on how to
> activate UUIDs (it's not an option in ./configure --help) and I cannot
> find the proper debian package for xalan. googled, and all.
> 
> do you have a list of the packages needed in order to compile blast
> with full features?
> 
> thank you
> 
> 
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Re: blast+ packaging

[Olivier Sallou]

hi,
after updating to your code, there is a compil (configure) error at
build time:

configure: error: Do not know how to build MT-safe with compiler
/usr/bin/g++

Maybe a missing dependency, do you have any idea?

Olivier

Le 5/29/11 6:12 PM, Aaron M. Ucko a écrit :
> Olivier Sallou  writes:
>
>> please feel free to commit in my dir. It will indeed be easier than merging.
> Done, thanks.  I also threw in some improvements to the copyright file that
> I'd meant to propose earlier:
>
> * Remove the stanza for (c++/)scripts/projects/xmlwrapp/*, whose LICENSE
>   file documents material absent from the ncbi-blast+ archive.
> * Adjust other upstream-related stanzas' Files specifications to prefix
>   c++/ and cover include in addition to src as appropriate.
>
>> For dir updates, be it ncbi-blast+ or ncbi-blast-plus, I would rather
>> like you update directly in my branch. We can, after that, "mv" the svn
>> dir to ncbi-blast+ once everything is ok from packaging point of view.
> That's fair, and no problem -- quite the contrary, when I was starting to
> commit to ncbi-blast+ (before the Alioth glitch and your latest reply), I
> didn't split my changes into individual commits quite as cleanly as I'd
> meant to, so re-committing them in ncbi-blast-plus gave me a good
> opportunity to correct that.
>
>> Please tell me once you have included your updates so that I recheck the
>> package on my side.
> I have.  Here are the remaining issues of which I'm aware, none of which
> should necessarily hold up an initial upload:
>
> * As previously mentioned, the linkage is still somewhat of a mess.
> * Also as mentioned, there are no individual manpages.
> * The standards version is slightly outdated; somebody should review the
>   upgrading checklist to see if advancing it requires any packaging changes.
> * As I recall, there was some interest in incorporating RMBLAST, the patch
>   for which risked changing the standard applications' behavior.  I expect
>   it should be possible to stay out of trouble by building it in a separate
>   copy of the source tree and linking it statically against any patched
>   libraries (and their reverse dependencies).
>
>> Regarding legacy, I prefered keeping it as separate package to avoid some
>> confusion and get it only if required on backward compatibility. Though,
>> if you think we should keep it in the same package, it is ok for me.
> OK, thanks for the explanation; I've kept the split.
>

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ubuntu backport on launchpad usage

[Olivier Sallou]

Hi,
I have 2 questions on ubuntu backport on debian-med launchpad:

1) can we put a package, simply to get it available on current ubuntu
version? (though deb package will be available on next ubuntu release).
If yes, how do we manage it from version point of view ? If debian
package has version xxx-2, on launchpad we should put xxx-2~lucid1 ?

2) How do we manage  changelog. Should we update svn changelog of the
package to add a ~lucid1 (for example) in the history then send the
package to launchpad, or should we get the source code, create a
specific changelog for launchpad and then send the package?

Thanks

Olivier

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Re: blast+ packaging

[Olivier Sallou]

LTLIBOBJS=''
LZO_INCLUDE=''
LZO_LIBS=''
MATH_LIBS=''
MT_SFX=''
MUPARSER_INCLUDE=''
MUPARSER_LIBS=''
MYSQL_INCLUDE=''
MYSQL_LIBS=''
NCBIATOMIC_LIB=''
NCBI_C_INCLUDE=''
NCBI_C_LIBPATH=''
NCBI_C_ncbi=''
NCBI_PLATFORM_BITS=''
NCBI_SSS_INCLUDE=''
NCBI_SSS_LIBPATH=''
NETWORK_LIBS=''
NETWORK_PURE_LIBS=''
NO_STRICT_ALIASING=''
OBJEXT='o'
ODBC_INCLUDE=''
ODBC_LIBS=''
OECHEM_INCLUDE=''
OECHEM_LIBS=''
OPENGL_INCLUDE=''
OPENGL_LIBS=''
OPENGL_STATIC_LIBS=''
OPENSSL_INCLUDE=''
OPENSSL_LIBS=''
OPENSSL_STATIC_LIBS=''
OPT_GROUPS=''
ORBACUS_INCLUDE=''
ORBACUS_LIBPATH=''
OSMESA_INCLUDE=''
OSMESA_LIBS=''
OSMESA_STATIC_LIBS=''
OSTYPE='linux-gnu'
PACKAGE_BUGREPORT='cpp-c...@ncbi.nlm.nih.gov'
PACKAGE_NAME='ncbi-tools++'
PACKAGE_STRING='ncbi-tools++ 0.0'
PACKAGE_TARNAME='ncbi-tools--'
PACKAGE_VERSION='0.0'
PATH_SEPARATOR=':'
PCREPOSIX_LIBS=''
PCRE_INCLUDE=''
PCRE_LIB=''
PCRE_LIBS=''
PNG_INCLUDE=''
PNG_LIBS=''
PROJECTS=''
PYTHON23=''
PYTHON23_INCLUDE=''
PYTHON23_LIBS=''
PYTHON24=''
PYTHON24_INCLUDE=''
PYTHON24_LIBS=''
PYTHON25=''
PYTHON25_INCLUDE=''
PYTHON25_LIBS=''
PYTHON=''
PYTHON_INCLUDE=''
PYTHON_LIBS=''
RANLIB=''
RESOLVER_LIBS=''
RPCSVC_LIBS=''
RT_LIBS=''
RUNPATH_ORIGIN=''
Rules=''
SABLOT_INCLUDE=''
SABLOT_LIBS=''
SABLOT_STATIC_LIBS=''
SGE_INCLUDE=''
SGE_LIBS=''
SHELL='/bin/bash'
SP_INCLUDE=''
SP_LIBS=''
SQLITE3_INCLUDE=''
SQLITE3_LIBS=''
SQLITE3_STATIC_LIBS=''
SQLITE_INCLUDE=''
SQLITE_LIBS=''
STATIC=''
STRIP=''
SYBASE_DBLIBS=''
SYBASE_DLLS=''
SYBASE_INCLUDE=''
SYBASE_LCL_PATH=''
SYBASE_LIBS=''
SYBASE_PATH=''
TAIL=''
TAIL_N=''
TCHECK_CL=''
THREAD_LIBS=''
TIFF_INCLUDE=''
TIFF_LIBS=''
TLS_INCLUDE=''
TLS_LIBS=''
UNGIF_INCLUDE=''
UNGIF_LIBS=''
UNIX_SRC=''
UNIX_USR_PROJ=''
UNLESS_PUBSEQOS=''
UNLESS_WITH_DLL=''
USUAL_AND_DLL=''
USUAL_AND_LIB=''
UUID_LIBS=''
VALGRIND_PATH=''
WXWIDGETS_GL_LIBS=''
WXWIDGETS_GL_STATIC_LIBS=''
WXWIDGETS_INCLUDE=''
WXWIDGETS_LIBS=''
WXWIDGETS_POST_LINK=''
WXWIDGETS_STATIC_LIBS=''
WXWIN_GL_LIBS=''
WXWIN_GL_STATIC_LIBS=''
WXWIN_INCLUDE=''
WXWIN_LIBS=''
WXWIN_POST_LINK=''
WXWIN_STATIC_LIBS=''
XALAN_INCLUDE=''
XALAN_LIBS=''
XALAN_STATIC_LIBS=''
XCONNEXT=''
XERCES_INCLUDE=''
XERCES_LIBS=''
XERCES_STATIC_LIBS=''
XPM_INCLUDE=''
XPM_LIBS=''
XSLTPROC=''
X_CFLAGS=''
X_EXTRA_LIBS=''
X_LIBS=''
X_PRE_LIBS=''
Z_INCLUDE=''
Z_LIB=''
Z_LIBS=''
_ACJNI_JAVAC=''
ac_ct_CC='gcc'
ac_ct_CXX='g++'
ac_ct_RANLIB=''
algo=''
app=''
bdb=''
bindir='${exec_prefix}/bin'
build='x86_64-unknown-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_root=''
build_vendor='unknown'
builddir=''
c_ncbi_runpath=''
check=''
compiler=''
compiler_root='/usr'
compiler_version='000'
configurables_mfname=''
datadir='${prefix}/share'
dbapi=''
dll_ext=''
exe_ext=''
exec_prefix='NONE'
f_compile=''
f_libpath=''
f_outexe=''
f_outlib=''
f_outobj=''
f_runpath=''
freetds=''
freetype_config=''
ftds64=''
gui=''
has_dll_loadable=''
host='x86_64-unknown-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='unknown'
includedir='${prefix}/include'
infodir='${prefix}/info'
internal=''
lib_ext=''
lib_l_ext=''
lib_l_pre=''
lib_pre=''
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
loadable_ext=''
local_lbsm=''
localstatedir='${prefix}/var'
make_shell=''
mandir='${prefix}/man'
mysql_config=''
ncbi_crypt=''
ncbi_runpath=''
ncbi_xreader_pubseqos2=''
ncbi_xreader_pubseqos=''
ncbicntr=''
obj_ext=''
objects=''
oldincludedir='/usr/include'
prefix='NONE'
program_transform_name='s,x,x,'
runpath=''
sbindir='${exec_prefix}/sbin'
script_shell=''
serial=''
serial_ws50_rtti_kludge=''
sharedstatedir='${prefix}/com'
signature=''
sra=''
srcdir='.'
sssutils=''
status_dir=''
sysconfdir='${prefix}/etc'
target_alias=''
top_srcdir=''
wxconf=''

## --- ##
## confdefs.h. ##
## --- ##

#define HOST "x86_64-unknown-linux-gnu"
#define HOST_CPU "x86_64"
#define HOST_OS "linux-gnu"
#define HOST_VENDOR "unknown"
#define NCBI_COMPILER "UNKNOWN"
#define NCBI_COMPILER_UNKNOWN 1
#define NCBI_COMPILER_VERSION 000
#define NCBI_CXX_TOOLKIT 1
#endif
#ifdef __cplusplus
extern "C" void exit (int) throw ();

configure: exit 1


Le 5/30/11 3:27 PM, Aaron Ucko a écrit :
> That's a puzzling error; please send your c++/config.log, which should shed 
> more light on it.  Thanks!
>
> -- Sent from my Palm Pre
> On May 30, 2011 3:44, Olivier Sallou <olivier.sal...@irisa.fr> wrote: 
>
> hi,
>
> after updating to your code, there is a compil (configure) error at
>
> build time:
>
>
>
> configure: error: Do not know how to build MT-safe with compiler
>
> /usr/bin/g++
>
>
>
> Maybe a missing dependency, do you have any idea?
>
>
>
> Olivier
>
>
>
> Le 5/29/11 6:12 PM, Aaron M. Ucko a écrit :
>
> > Olivier Sallou <olivier.sal...@irisa.fr> writes:
>
> >
>
> >> please feel free to commit in my dir. It will indeed be easier than 
> merging.
>
> > Done, thanks.  I also threw in some improvements to the copyright file 
> that
>
> > I'd meant to propose earlier:
>
> >
>
> > * Remove the stanza for (c++/)scripts/projects/xmlwrapp/*, whose LICENSE
>
> >   file documents material absent from the ncbi-blast+ archive.
>
> > * Adjust other upstream-related stanzas' Files specifications to prefix
>
> >   c++/ and cover include in addition to src as appropriate.
>
> >
>
> >> For dir updates, be it ncbi-blast+ or ncbi-blast-plus, I would rather
>
> >> like you update directly in my branch. We can, after that, "mv" the 
> svn
>
> >> dir to ncbi-blast+ once everything is ok from packaging point of 
> view.
>
> > That's fair, and no problem -- quite the contrary, when I was starting to
>
> > commit to ncbi-blast+ (before the Alioth glitch and your latest reply), I
>
> > didn't split my changes into individual commits quite as cleanly as I'd
>
> > meant to, so re-committing them in ncbi-blast-plus gave me a good
>
> > opportunity to correct that.
>
> >
>
> >> Please tell me once you have included your updates so that I recheck 
> the
>
> >> package on my side.
>
> > I have.  Here are the remaining issues of which I'm aware, none of which
>
> > should necessarily hold up an initial upload:
>
> >
>
> > * As previously mentioned, the linkage is still somewhat of a mess.
>
> > * Also as mentioned, there are no individual manpages.
>
> > * The standards version is slightly outdated; somebody should review the
>
> >   upgrading checklist to see if advancing it requires any packaging 
> changes.
>
> > * As I recall, there was some interest in incorporating RMBLAST, the 
> patch
>
> >   for which risked changing the standard applications' behavior.  I 
> expect
>
> >   it should be possible to stay out of trouble by building it in a 
> separate
>
> >   copy of the source tree and linking it statically against any patched
>
> >   libraries (and their reverse dependencies).
>
> >
>
> >> Regarding legacy, I prefered keeping it as separate package to avoid 
> some
>
> >> confusion and get it only if required on backward compatibility. 
> Though,
>
> >> if you think we should keep it in the same package, it is ok for me.
>
> > OK, thanks for the explanation; I've kept the split.
>
> >
>
>
>

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Re: blast+ packaging

[Olivier Sallou]

Hi,

I tried debuild -rfakeroot
but it still fails. I cannot build anymore the package.

 dpkg-source -b ncbi-blast-2.2.25+-src
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: warning: patches have not been applied, applying them now
(use --no-preparation to override)
dpkg-source: info: applying legacy_rename_rpsblast
dpkg-source: info: applying fix_checks
dpkg-source: info: applying fix_gcc46_errors
dpkg-source: info: building ncbi-blast+ using existing
./ncbi-blast+_2.2.25.orig.tar.gz
dpkg-source: info: building ncbi-blast+ in
ncbi-blast+_2.2.25-1.debian.tar.gz
dpkg-source: internal error: add_directory() only handles directories
dpkg-buildpackage: error: dpkg-source -b ncbi-blast-2.2.25+-src gave
error exit status 29

Olivier

Le 5/30/11 7:23 PM, Aaron M. Ucko a écrit :
> Olivier Sallou  writes:
>
>> configure: error: Do not know how to build MT-safe with compiler
>> /usr/bin/g++
> Updating debian/rules to r6893 should fix that, though I'd still
> recommend using fakeroot only as needed (e.g., via debuild -rfakeroot).
>
> Once again, thanks for pointing out the problem and sorry you ran into it.
>

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inclusion of binaries+source in package question

[Olivier Sallou]

Hi, 
I have a question regarding inclusion of source code of other packages. 
In biomaj watcher, I need to include some binaries due to missing gwt2 package 
(and task too hard for the moment for me to package it). 
As such, with their license, source code must be available. 


My concern is source is very, very large (and must be cleanup because it 
contains prebuild libraries). 
Does source MUST be included in my source package, or could a link to svn URLs 
in README be ok? 


Thanks 


Olivier 

Re: inclusion of binaries+source in package question

[Olivier Sallou]

Hi,
I have included required Notice files and source (for smartgwt which is LGPL) 
in biomaj-watcher source.
So package should be ok now for upload.

You may however change the target in control file to contrib/non-free as well 
as section "unstable vs experimental"

I will upload biomaj and watcher to PPA this summer.

Thanks

Olivier

- Mail original -
> De: "Steffen Möller" 
> À: "Olivier Sallou" 
> Envoyé: Vendredi 3 Juin 2011 02:43:34
> Objet: Fwd: Re: inclusion of binaries+source in package question
> Good news. Sorry for my wrong advise.
> Steffen
> 
>  Original Message 
> Subject: Re: inclusion of binaries+source in package question
> Resent-Date: Fri, 3 Jun 2011 00:18:05 + (UTC)
> Resent-From: debian-med@lists.debian.org
> Date: Fri, 3 Jun 2011 09:17:41 +0900
> From: Charles Plessy 
> To: debian-med@lists.debian.org
> 
> Le Thu, Jun 02, 2011 at 09:04:44AM +0200, Olivier Sallou a écrit :
> > .
> > In biomaj watcher, I need to include some binaries due to missing
> > gwt2 package (and task too hard for the moment for me to package
> > it).
> > As such, with their license, source code must be available.
> 
> Bonjour Olivier,
> 
> correct me if I am wrong, but if the GWT2 package is only distributed
> under the
> Apache 2.0 license, as debian/copyright indicates, there is no need to
> redistribute its source code.
> 
> http://www.apache.org/licenses/LICENSE-2.0.html
> 
> However, pay attention that this license requires us to distribute
> copies of
> the NOTICE files that may be here and there, not only in GWT's root
> directory.
> 
> Have a nice day,
> 
> --
> Charles Plessy
> Debian Med packaging team,
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan
> 
> 
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svn alioth issue

[Olivier Sallou]

Hi,
I tried to rename one dir (ncbi-blast-plus to ncbi-blast+) with svn rename.
On commit I have an error:

#svn commit -m "move ncbi-blast-plus to ncbi-blast+" ncbi-blast+
Adding ncbi-blast+
Adding ncbi-blast+/trunk
svn: Commit failed (details follow):
svn: Can't create directory
'/svn/debian-med/db/transactions/6917-1.txn': Read-only file system

(svn status shows: A  +ncbi-blast+ )

Any idea?

Thanks

Olivier

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Re: svn alioth issue

[Olivier Sallou]

I have:
URL:
svn+ssh://osallou-gu...@scm.alioth.debian.org/svn/debian-med/trunk/packages
Repository Root:
svn+ssh://osallou-gu...@scm.alioth.debian.org/svn/debian-med

Is it due to migration?

Issue is that svn switch does not work for svn+ssh but HTTP only

Olivier

Le 6/6/11 4:32 PM, Thorsten Alteholz a écrit :
> Hi Olivier,
>
> On Mon, 6 Jun 2011, Olivier Sallou wrote:
>> I tried to rename one dir (ncbi-blast-plus to ncbi-blast+) with svn
>> rename.
>> On commit I have an error:
>
> can you please check whether you try to commit to alioth.debian.org or
> svn.debian.org? In case it is alioth, you will get this error. On that
> host the repositories are mounted readonly. You need to 'svn switch'
> to svn.debian.org.
>
>   Thorsten
>
>

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First upload of ncbi-blast+

[Olivier Sallou]

Hi,
the package ncbi-blast+ should be ready for a first upload.
Aaron made some modifications on my first packaging, and I retested it.

I renamed the directory in svn tree (trunk/packages) to ncbi-blast+
instead of ncbi-blast-plus.

Can someone have a look and upload to ftp master ?

Thanks

Olivier

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launchpad question

[Olivier Sallou]

HI,
I have an other question to put a package on launchpad.
My package is already on Ubuntu, but for next release (oneiric).

To make it available on current version, I tried to repackage it using a
different version (-0).
However, when using dput, I have an email error telling me that orig
file is already in Primary archive.
How can I ask to build existing data on a previous release?

Thanks

Olivier

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Re: launchpad question

[Olivier Sallou]

option -sd was what I needed,

thanks

Olivier

Le 6/7/11 12:33 PM, Charles Plessy a écrit :
> Le Tue, Jun 07, 2011 at 11:23:45AM +0200, Olivier Sallou a écrit :
>> To make it available on current version, I tried to repackage it using a
>> different version (-0).  However, when using dput, I have an email error
>> telling me that orig file is already in Primary archive.  How can I ask to
>> build existing data on a previous release?
> i Olivier,
>
> it is a bit difficult to answer without knowing which package you are working
> on, but my guess is that if you use a debian revision number lower than 1, 
> then
> the Debian changes file (‘.changes’) will contain an entry for the original
> upstream tarball (‘.orig.tar.gz|bz2’), and if in your PPA or in Ubuntu there 
> is
> already a source package using this tarball, the upload will be rejected.  The
> solution is then to pass -sd at the generation of the source package, or to
> delete the entry by hand before signing your upload.
>
> Cheers,
>

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Re: SPAM from launchpad (Was: [Build #2552982] i386 build of biomaj 1.1.0-0~lucid1 in ubuntu lucid RELEASE (debian-med PPA))

[Olivier Sallou]

I am trying to build biomaj on launchpad, but I have some issues with a
non deleted packaged on ppa due to a previous error.
Maybe you receive emails because you was the uploader of the package
Don't know how they select the email address

Olivier

Le 6/8/11 2:14 PM, Andreas Tille a écrit :
> Hi,
>
> I wonder what might be the reason that I get several mails from
> launchpad to my tille@d.o address.  Any way to stop this?
>
> Kind regards
>
>Andreas.
>
> - Forwarded message from Launchpad Buildd System  
> -
>
> To: ti...@debian.org
> From: Launchpad Buildd System 
> Subject: [Build #2552982] i386 build of biomaj 1.1.0-0~lucid1 in ubuntu lucid
>   RELEASE (debian-med PPA)
> Date: Wed, 08 Jun 2011 11:57:15 -
> X-Spam_score: -6.3
>
>
>  * Source Package: biomaj
>  * Version: 1.1.0-0~lucid1
>  * Architecture: i386
>  * Archive: debian-med PPA
>  * Component: main
>  * State: Failed to upload
>  * Duration: four minutes
>  * Build Log: 
> https://launchpad.net/~debian-med/+archive/ppa/+build/2552982/+files/buildlog_ubuntu-lucid-i386.biomaj_1.1.0-0%7Elucid1_BUILDING.txt.gz
>  * Builder: https://launchpad.net/builders/thallium
>  * Source: not available
>
> Upload log:
> Uploading build 20110608-115702-PACKAGEBUILD-2552982 failed.
>
> If you want further information about this situation, feel free to
> contact a member of the Launchpad Buildd Administrators team.
>
> --
> i386 build of biomaj 1.1.0-0~lucid1 in ubuntu lucid RELEASE
> https://launchpad.net/~debian-med/+archive/ppa/+build/2552982
>
>
> - End forwarded message -
>

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bioperl

[Olivier Sallou]

Hi Charles,
I see your are the maintainer of bioperl, do you plan to go to version
1.6.901 ?

This version is available on CPAN, and is required to further updates of
gbrowse

Thanks

Olivier

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circular dependencies question

[Olivier Sallou]

Hi,
in my gbrowse packaging, after upload to unstable, I see a circular
dependency error.
It occurs on libwww-perl (which contains circular dependency).

Are circular dependencies an issue?

I also have an other "error" on perlapi shown as unknown (see below).
I do not specify in my control file any perlapi dependency (certainly
done via perl

gbrowse-calign
 (Debian Med
Packaging Team )

* dependency perl
   is
  successfully-tested
* dependency perlapi-5.10.1 is /unknown/
* dependency libc6
   is
  essential-required
* dependency gbrowse
   
is /circular-dependency/

I see the same error on other packages.
Same question, is it an issue?

Thanks

Olivier

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Bug#632086: ITP:libmath-vecstat-perl --Some basic numeric stats on vectors

[Olivier Sallou]

Package: wnpp
Severity: wishlist
X-Debbugs-CC:debian-med@lists.debian.org

Language: Perl
Homepage: http://search.cpan.org/dist/Math-VecStat/
Description: This package offers some basic statistics on vectors
(min,max,average,)
Dependencies: None
Upstream author: Andrea Spinelli

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Bug#632174: ITP:circos -- software package for visualizing data and information in a circular layout

[Olivier Sallou]

Package: wnpp
Severity: wishlist
X-Debbugs-CC:debian-med@lists.debian.org

Language: Perl
Homepage: http://circos.ca/
Description: Circos is a software package for visualizing data and
information <http://circos.ca/intro/data_visualization>. It visualizes
data in a circular layout <http://circos.ca/intro/circular_approach> ---
this makes Circos ideal for exploring relationships between objects or
positions
Upstream author: Martin Krzywinski 


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Re: Bug#632174: ITP:circos -- software package for visualizing data and information in a circular layout

[Olivier Sallou]

Hi,
I have issues with reportbug.
I do not know why, but program is ok, but mail never sent (I never have
any answer).

I will add license info.

regarding taks, I think so. Circos is used by many
biologists/bioinformatians to represent genes (etc..) and relations
using its circular representation.

While not limited to bioinformatics, it comes from this domain and is
widely used by the communauty.

regards

Olivier

Le 6/30/11 11:55 AM, Andreas Tille a écrit :
> it your ITPs.  Your quotes look quite different from the
> usual template (in sequence and the fields used - for instance License
> field is missing).
>
> Regarding the package itself: Do you consider it worth mentioning on
> our tasks page?  The relation to Bi

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need sponsor to upload Circos

[Olivier Sallou]

Hi,
Circos is ready for review/upload on svn.
Could someone have a look and upload it ?

It depends on libmath-vecstat-perl, which just passed to unstable.

There is no lintian warning and pbuilder is ok.

Warning: regarding source, I added a warning in readme.source. Indeed,
remove sources (tar.gz) are not complete packages. There is a "main"
package and one (or more) patch package. Additionally, main package
contains a few tools, but an other "source" package contains again those
tools plus additional ones (could be newer than main ones).
So one need to get main source, apply patches, add tools then apply
tools patches

So, to avoid this stuff to get orig.tar.gz, if you want me to make it
available, please let me know.

thanks

Olivier

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problem with web site http://packages.debian.org/

[olivier sallou]

Hi,
there is an issue with one of my packages with the displayed description.

http://packages.debian.org/sid/biomaj

It displays:


Binary utilities supporting TI's MSP430 targetsPackage: biomaj (1.1.0-3)

The programs in this package are used to manipulate binary and object files
that may have been created for TI's MSP430 architecture. This package is
primarily intended for MSP430 developers and cross-compilers.

***

Though, the description is not at all the correct one . The problem occured
after my package update from 1.1.0-2 to 1.1.0-3. Previous one was correct.

Sometimes, after forcing a refresh in my navigator, the web site shows me
the "old" version 1.1.0-2.(with the correct description), even though
the version 1.1.0-3 is present (
http://ftp.de.debian.org/debian/pool/main/b/biomaj/). Maybe a mirroring
issue?

I checked my description in control file and it is correct (I downloaded the
file from debian ftp site to be sure)


Can someone drive me to the correct person to contact?


Thanks


Olivier

circos packaging upload

[Olivier Sallou]

Hi,
sorry to ping again, but I got no answer from my previous mail to get a
sponsor to upload/check Circos package.

I am not in a hurry to do so, but I'd like to know that someone will take this 
in charge.

Thanks

Olivier

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Re: circos packaging upload

[Olivier Sallou]

Hi Andreas,
as I said in my previous email, upstream source is quite a mess.
One need to mix several packages (not with the same version) and apply
"patches" which are in fact some tar files containing only modified
files

I explained this in readme.source.

To avoid this mess, if you want, I can make the orig.tar.gz I created
from upstream source available for download so that you get it.

Olivier

Le 7/13/11 9:08 AM, Andreas Tille a écrit :
> On Wed, Jul 13, 2011 at 08:58:50AM +0200, Olivier Sallou wrote:
>> sorry to ping again, but I got no answer from my previous mail to get a
>> sponsor to upload/check Circos package.
> $ uscan --verbose --force-download
> -- Scanning for watchfiles in .
> -- Found watchfile in ./debian
> -- In debian/watch, processing watchfile line:
>http://circos.ca/distribution/circos-(.*).tar.gz
> uscan warning: In watchfile debian/watch, reading webpage
>   http://circos.ca/distribution/ failed: 403 Forbidden
> -- Scan finished
>
> Any better way to fetch the source tarball?
>
> Kind regards
>
> Andreas. 
>

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Re: circos packaging upload

[Olivier Sallou]

I will have a look for the get-orig-source to try to recreate the
complete stuff automatically.
This will be quite difficult I think but I will try.

Let's wait for the moment.
I will let you know

Thanks

Olivier

Le 7/13/11 10:08 AM, Andreas Tille a écrit :
> d s/0.54\.1-1

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Re: circos packaging upload

[Olivier Sallou]

Hi Andreas,
I succeeded at creating a get-orig-source that gets everything.
I just hope it will be fine with next updates (some files are tgz or
tar.gz...).

In the meanwhile the get-orig-source creates the orig file with the
incremental copy stuff.

So it should be fine now.

Thanks

Olivier

Le 7/13/11 10:08 AM, Andreas Tille a écrit :
> On Wed, Jul 13, 2011 at 09:12:38AM +0200, Olivier Sallou wrote:
>> as I said in my previous email, upstream source is quite a mess.
>> One need to mix several packages (not with the same version) and apply
>> "patches" which are in fact some tar files containing only modified
>> files
> Ahhh, now I remember.
>  
>> To avoid this mess, if you want, I can make the orig.tar.gz I created
>> from upstream source available for download so that you get it.
> Well, you explained that this is a mess - but you need to provide a
> reproducible way for others to get the orig.tar.gz.  As a precondition
> we need at least a *working* watch file (just commited).
>
> Remark:  When dealing with R packages which are frequently featuring a
> '-' sign in their version I learned the hard way that it is better to
> take over this versioning scheme.  For the moment I took over this also
> in circos and did s/0.54\.1-1/0.54-1-1/ in the changelog as package
> version.  I'm not specifically keen on this change.  However, if you
> prefer the '.' versioning scheme for upstream version you need to
> prepend the string in debian/watch by
>
>   opts="dversionmangle=s/\./-/" \
>
> or alternatively
>
>   opts="uversionmangle=s/-/./" \
>
> to let uscan detect the proper version.
>
> This serves us with the latest patch set for circos.  The proper way
> to do is now to write a get-orig-source script which iterates down the
> versions to the main release, fetches those tarballs and applies the
> patches.  Well, this is a bit of tricky work but it makes cooperation
> and sponsoring and finally your own life easier for the future.
>
> If you are in a hurry we can cowardly work around this for a moment and
> you upload your orig.tar.gz to mentors.debian.net.  But please in this
> case add a get-orig-source target in debian/rules which echos clear
> advise (or cat README.Source or something like this).  Otherwise people
> might ignore this.
>
> Kind regards
>
> Andreas.
>
> PS: Alternatively you might want to talk to upstream whether they might
> imagine to follow the release habits of so many other projects ...
>

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circos packaging

[Olivier Sallou]

Hi Andreas, 
the reference is to the package libmath-vecstat-perl. 
I packaged it some days ago and gone to sid recently (in debian perl group) 
I did an apt-get update and could install it. 


Olivier 

circos: missing dep

[Olivier Sallou]

Hi, indeed, dependency was missing (which is quite surprising as I did myself 
the package for this dependency) I missed it as it is not required for 
building and already installed on my computer. 
Thank you for adding it, I won't be able to do so before at least Thursday. 
Monday or later will be fine, there is no urgent need. 
Olivier 

On Fri, Jul 15, 2011 at 06:31:38PM +0200, Olivier Sallou wrote: 

> the reference is to the package libmath-vecstat-perl. Ahh, I might need to 
> apt-file update.  So I will add this dependency.

HOwever, this will not happen before Monday.

Kind regards

   Andreas. 
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circos licensing issues

[Olivier Sallou]

Hi,
I have contacted upstream author, and he will remove copyright issues on
fonts in next version (that should come soon).
By the way, upstream patches will contain full code, making easier to
format original source code for packaging.
So I propose to wait for the next version for the package. I will check
it and let you know for further upload.

Thanks

Olivier

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Re: circos licensing issues

[Olivier Sallou]

Thanks,
I will let you know.
I just contacted him on a remaining issue. There is the pragmata font in the 
package but I am not sure of the copyright on this one.
Other copyright issues have been fixed.

Once this is solved, I will go for the packaging (almost done).

Olivier

- Mail original -
> De: "Shaun Jackman" 
> À: "Olivier Sallou" 
> Cc: "Andreas Tille" , "Debian Med Project List" 
> 
> Envoyé: Lundi 25 Juillet 2011 19:58:09
> Objet: Re: circos licensing issues
> Hi all,
> 
> I work with the author of Circos and am a Debian developer. I'm happy
> to help if you need a contact inside.
> 
> Cheers,
> Shaun
> 
> On 21 July 2011 22:33, Olivier Sallou  wrote:
> > Hi,
> > I have contacted upstream author, and he will remove copyright
> > issues on
> > fonts in next version (that should come soon).
> > By the way, upstream patches will contain full code, making easier
> > to
> > format original source code for packaging.
> > So I propose to wait for the next version for the package. I will
> > check
> > it and let you know for further upload.
> >
> > Thanks
> >
> > Olivier
> >
> > --
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> > IRISA / University of Rennes 1
> > Campus de Beaulieu, 35000 RENNES - FRANCE
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> >
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> >
> >
> >
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circos for packaging

[Olivier Sallou]

Hi andreas,
upstream author made requested changes on copyright (change some fonts)
and a few packaging updates that ease our packaging.

Now, there are 3 packages:
- circos and circos-fonts, both from the circos directory in alioth

- circos-tools in the circos-tools directory in alioth (a Recommends of circos)


The get-orig-source is easier than before, only one download is required (no 
more 1 package then apply patches...).

Regarding circos-fonts, Circos embeds some partial fonts (those it needs). 
Those fonts are not available as Debian package. SO I hope it won't be an issue 
to create a sub-package for this (installed under circos directories).

Can you please upload those?


Olivier

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Re: circos packaging

[Olivier Sallou]

Hi, for Computer Modern Unicode fonts, I am having a look to package it 
independently. Where did you see that other fonts do not allow modification? I 
see no such mention in text files. 
Olivier 

Le Wed, Jul 27, 2011 at 05:59:15PM +0900, Charles Plessy a écrit : 

I have interest in Circos, but I can not promise to be fast.  But if nobody 
stemps in,
I will eventually review the package.  This said, I also think that properly 
packaging
the fonts separately would be a plus.  This is very well organised, see 
http://pkg-fonts.alioth.debian.org/ Hi Olivier,

I looked at the fonts more in details.  circlethings, circlethings2, pointers
and shapes do not allow modification, so we will need to either remove them
from the circos or distribute it in non-free.  I did not have time to verify
how essential they are.  symbols is Free and is part of Circos.  The ‘Computer
Modern Unicode fonts’ are an independant Free project that was already
requested for packaging ( http://bugs.debian.org/620537 ).  In the end, only 
this
one would benefit from being independantly packaged.

Have a nice day, 
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biomaj-watcher reupload

[Olivier Sallou]

Hi Steffen, 
could you please reupload bmaj watcher? 


I will try to have a look at Chado for packaging during August. 


Thanks 


Olivier 

Re: circos packaging

[Olivier Sallou]

hi Charles,
I am dealing with upstream fonts author and upstream author to try to
fix this.
For pointers font, author should be ok to relicense.
For shapes and circles, I don't think so.

So either upstream author can use other fonts, or I should package those
independently in non-free and put them in Suggests,
as those fonts are not mandatory for the software. Fonts are
configurable, and "basic" usage does not require at all those fonts.

I will let you know

For modern computer, I am currently packaging it with the Font team support.

Olivier

Le 8/1/11 9:43 AM, Charles Plessy a écrit :
> Le Mon, Aug 01, 2011 at 09:11:07AM +0200, Olivier Sallou a écrit :
>> Where did you see that other fonts do not allow modification?
>> I see no such mention in text files.
> Hi Olivier,
>
> this is exactly the problem: if it is not mentionned, it may not be allowed.
> In particular for fonts, I think that the doubt is strong, and I guess that 
> the
> FTP team will object similarly.  The best would be to ask for a clarification
> to the copyright holders (and ask them if they want to relicense them under
> DFSG-free terms, if we are lucky, they might say yes).
>
> Have a nice day,
>

-- 
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95

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Re: BLAST+ speed & build issues

[Olivier Sallou]

Hi Tim,
regarding speed, I don't know the reason of the difference between
static and dynamic linking here.
When I created the package I 've chosen the dynamic solution to reduce
the size of the binary, while making the library available for other
software linkage.
Creating a "static" package would be easy, but would double the size
(which is large) for blast+ on servers, and it could be confusing for
the user, no? (selecting between dynamic and static).


Olivier


Le 8/2/11 6:53 PM, Tim Booth a écrit :
> Hi Olivier and Aaron,
>
> I've been playing around with BLAST+, trying to tackle one fairly simple
> but unimportant issue and one more complex and problematic issue.
>
> The easy one first:
>
> In the build log (on Launchpad) I see that during the test phase of the
> build there are various attempts to connect to the NCBI servers -
> starting at:
>
> ==
> blast_services_unit_test
> ==
>
> Running 23 test cases...
> Error: (311.22) SOCK#1000[?]: [SOCK::Connect]  Failed 
> SOCK_gethostbyname("www.ncbi.nlm.nih.gov")
> Error: (303.7) [URL_Connect]  Socket connect to www.ncbi.nlm.nih.gov:80 
> failed: Unknown
> Error: (311.22) SOCK#2000[?]: [SOCK::Connect]  Failed 
> SOCK_gethostbyname("www.ncbi.nlm.nih.gov")
> Error: (303.7) [URL_Connect]  Socket connect to www.ncbi.nlm.nih.gov:80 
> failed: Unknown
> Error: (311.22) SOCK#3000[?]: [SOCK::Connect]  Failed 
> SOCK_gethostbyname("www.ncbi.nlm.nih.gov")
> Error: (303.7) [URL_Connect]  Socket connect to www.ncbi.nlm.nih.gov:80 
> failed: Unknown
> Error: (310.5) [blast4]  Cannot locate server
> Error: (315.1) Cannot connect to service "blast4"
> Error: (315.2) CConn_Streambuf::CConn_Streambuf(): NULL connector (UNKNOWN): 
> Unknown
>
> ...etc.
>
> These don't break the build but they should really be disabled.  Is
> there an easy way to do this, do you think?  I've had a poke around in
> the Makefiles but it's fairly cryptic.
>
> Anyway, the complex issue:
>
> A user reported that his analysis took an order of magnitude longer
> after upgrading BLAST+ (from the static binary build to the Debian Med
> build).  I'd expect some slowdown with dynamic linking but this is
> indeed fairly drastic:
>
> Static (downloaded from NCBI):
> tbooth@barsukas[latest]time bash -c 'for (( c=1; c<=50; c++ )) ; do 
> ~/tings/ncbi-blast-2.2.25+/bin/blastx -h > /dev/null ; done'
> 0.76user 0.29system 0:00.94elapsed 110%CPU (0avgtext+0avgdata 
> 39728maxresident)k
> 32inputs+0outputs (2major+133193minor)pagefaults 0swaps
>
> Dynamic (built with debuild):
> tbooth@barsukas[latest]time bash -c 'for (( c=1; c<=50; c++ )) ; do 
> c++/BUILD/bin/blastx -h > /dev/null ; done' 
> 3.91user 8.91system 0:13.00elapsed 98%CPU (0avgtext+0avgdata 
> 827376maxresident)k
> 0inputs+0outputs (0major+2623550minor)pagefaults 0swaps
>
> So assuming that printing the help message is trivial, and essentially a
> no-op, the Debian build is taking more than a quarter of a second to
> fire up.  For scripts that call BLAST in a tight loop on small sequences
> this is a drastic slowdown - nearly all the analysis time is actually
> used up just starting BLAST.
>
> For comparison, I tried timing Perl:
>
> tbooth@barsukas[latest]time bash -c 'for (( c=1; c<=50; c++ )) ; do perl -h > 
> /dev/null ; done'
> 0.36user 0.17system 0:00.21elapsed 244%CPU (0avgtext+0avgdata 
> 6064maxresident)k
> 0inputs+0outputs (0major+27317minor)pagefaults 0swaps
>
> I know Perl is well optimised, but this is still a massive disparity.
>
> I wondered if there was a way to speed up linking, so I had a play with
> 'prelink', but I realised this just helps starting the program the first
> time in the loop.  After that the linking data is all cached anyway.
> Then I tried mashing all the .so files created by the build into one
> "libncbiblast_all.so" and linking to this.  It compiled and ran but made
> no difference whatsoever to startup time of blastx.
>
> So, maybe I'm barking up the wrong tree and something other than the
> linking is causing the delay, or maybe there is just no way to get the
> speedup other than statically linking the binaries.  (I know I can't be
> the first person to try all this but I can't find any previous
> discussion/documentation).
>
> If the latter, I know the real fix is for script authors use BLAST more
> sensibly, but I'm wondering if there is any mileage in trying to make a
> ncbi-blast+-static package?  This would build from the 

Re: Blog about Debian Med BOF

[Olivier Sallou]

furthermore, regarding biomed, there are some others such naming such as
Biomed central for publications
People could thing there is a link.

Olivier

Le 8/3/11 2:04 PM, Andreas Tille a écrit :
> Hi Tony,
>
> On Wed, Aug 03, 2011 at 12:18:23PM +0100, Tony Travis wrote:
>> I said that "Debian Med" is quite misleading, and suggested changing it  
>> to "Debian Biomed", which more accurately reflects the target audience.
> Renaming an existing project is a *big* and *time consuming* effort.
> In any case I would avoid this (I've been there).
>
> I'm also not convinced that Biomed is as well as missleading if you are
> coming from the medical imaging or medical practice side.  We are not
> only doing biology stuff inside the project.
>
>> However, there seemed to be little support for this idea...
> IMHO this is for the two reasons mentioned above.
>
> Kind regards
>
>  Andreas.
>

-- 
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (pgp.mit.edu)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438



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