Re: RFS: tex4ht

[Filippo Rusconi]

Hi, 

I cannot help you (not a DD nor very experienced), but I see that you
are having hard time to find a sponsor for this package. May I just
tell that I use that software with a lot of satisfaction. I'd like to
see a new version in Debian. 

I hope some DD will help you with this package.

Ciao,

Filippo


On Fri, Dec 09, 2005 at 08:48:14AM +0530, Kapil Hari Paranjape wrote:
> Dear Sponsors,
> 
> I am the non-DD maintainer of tex4ht and have been looking for 
> a sponsor for the package at
> 
>   http://www.imsc.res.in/~kapil/tex4ht/tex4ht/tex4ht_20051130-1.dsc
>   or
>   http://mentors.debian.net/pool/main/t/tex4ht/tex4ht_20051130-1.dsc
> 
> The package has not seen an upload since the release of sarge.
> 
> Details follow.
> 
> Regards,
> 
> Kapil.
> ==pkg details for tex4ht
> Source: tex4ht
> Binary: tex4ht tex4ht-common
> Architecture: source any all
> Version: 20051130-1
> Maintainer: Kapil Hari Paranjape <[EMAIL PROTECTED]>
> Changed-By: Kapil Hari Paranjape <[EMAIL PROTECTED]>
> Description: 
>  tex4ht - LaTeX and TeX for Hypertext (HTML) - executables
>  tex4ht-common - LaTeX and TeX for Hypertext (HTML) - support files
> Closes: 219482 303658 315992 320933 320968 339593
> Changes: 
>  tex4ht (20051130-1) unstable; urgency=low
>  .
>* New upstream release (2005-11-30-22:55).
>   - No lonely  tags. Closes: #320968.
>   - Handle Scandinavian Characters better.
> Closes: #320933.
>   - Handle embedded images better. Closes #340296.
>   - Include support for eTeX and conTeXt.
> Closes #311523.
>   - Give user the option of avoiding unicode
> ligatures. Closes #307647.
>* Removed all alternatives providing ht. Closes: #303658.
>* The html files from the web-site are not included with
>  the packages. Instead added an introductory html document
>  generated from LaTeX with source. Closes: #219482.
>* The arch-independent files put in a separate package.
>  This complies with section 6.7.5 in the developer's
>  reference.
>* Added some clarifications to the man page regarding
>  optional arguments for the scripts. Closes: #315992.
>* Added "Suggests: zip". Closes: #339593.
>* Standards Version bumped to 3.6.2.
>* Debhelper Version bumped to 4.
>* Dropped the "time" portion of the upstream version
>  number when converting to Debian numbering.
> Files: 
>  35d4d0a901dfed6e83f2d26171dfd466 614 tex optional tex4ht_20051130-1.dsc
>  9d4d47585824fceeefd3ec46be33fe83 2946488 tex optional 
> tex4ht_20051130.orig.tar.gz
>  2497d9c08ef7fba295c6a895fff71f82 86215 tex optional tex4ht_20051130-1.diff.gz
> 
> ==end pkg details for tex4ht



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Filippo Rusconi, PhD - CNRS researcher - key C78F687C @ pgp.mit.edu

Author of ``GNU polyxmass'' at http://www.polyxmass.org

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Re: Bug#521918: pbuilder --build --binary-arch invokes 'build' target

[Filippo Rusconi]

On Mon, May 11, 2009 at 02:11:18PM +0200, Julien Cristau wrote:
> 
> On Mon, May 11, 2009 at 13:46:30 +0200, Lionel Elie Mamane wrote:
> 
> > No, policy is very clear on that: if you call the "build" target, you
> > _must_ satisfy Build-Depends-Indep and Build-Conflicts-Indep:
> > 
> And policy is clearly not followed by any actual practice on this point.
> So that's as much a bug in policy as anything else (#374029).
> 
> Cheers,
> Julien

Well, but then, why have new packagers trained by studying the Policy?

Look at my own situation (which must not be a rare one, I suppose):
I've worked to make a Debian package of the software I develop [0]
with the idea that the Debian Policy had to be implemented in the
package making.

That software recently entered Debian through NEW and almost
immediately after that I got a FTBFS bug report [2]: pbuilder called
debian/rules build without installing the required

Build-Depends-Indep: texlive-latex-extra, texlive-latex-recommended, 
texlive-fonts-recommended

which of course failed because pdflatex was not found on the system
and thus could not build the LaTeX docs of the software.

It is a pity to have a Debian Policy so well documented, to point
package-making learners to that Policy and then have non-conformant
builders.

In fact, I'd ask what would be the solution to overcome the problem
(apart from the desirable fixing the builders)?

My 2 eurocents,

Best regards,

Filippo


[0] http://massxpert.org
[1] http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=528086

--
Filippo Rusconi, PhD - CNRS - public key C78F687C
Author of ``massXpert'' at http://www.massxpert.org


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Re: Bug#521918: pbuilder --build --binary-arch invokes 'build' target

[Filippo Rusconi]

On Mon, May 11, 2009 at 03:52:07PM +0200, Giacomo A. Catenazzi wrote:
>
> Filippo Rusconi wrote:
>> On Mon, May 11, 2009 at 02:11:18PM +0200, Julien Cristau wrote:
>>> On Mon, May 11, 2009 at 13:46:30 +0200, Lionel Elie Mamane wrote:
>>>
>>>> No, policy is very clear on that: if you call the "build" target, you
>>>> _must_ satisfy Build-Depends-Indep and Build-Conflicts-Indep:
>>>>
>>> And policy is clearly not followed by any actual practice on this point.
>>> So that's as much a bug in policy as anything else (#374029).
>>>
>>> Cheers,
>>> Julien
>>
>> Well, but then, why have new packagers trained by studying the Policy?
>
> Because they should find errors in policy and report such bugs ;-)
>
> Really many bug of debian-policy are found by new maintainers,
> but unfortunately most of new maintainers are too shy to report
> bugs to debian-policy, just because they are *new* maintainers.
> Thus debian-policy still have many bugs.


Does this mean that you too think that on the specific matter dealt
with in this thread, it is the policy that is bugged and not the
autobuilders ? Or should I intersperse your message with smileys :)


Best regards,
 Filippo

--
Filippo Rusconi, PhD - CNRS - public key C78F687C
Author of ``massXpert'' at http://www.massxpert.org


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Re: Bug#521918: pbuilder --build --binary-arch invokes 'build' target

[Filippo Rusconi]

On Mon, May 11, 2009 at 08:34:54PM +0200, Petr Pudlak wrote:
> 
> On Mon, May 11, 2009 at 03:11:22PM +0200, Filippo Rusconi wrote:
> > 
> > It is a pity to have a Debian Policy so well documented, to point
> > package-making learners to that Policy and then have non-conformant
> > builders.
> > 
> > In fact, I'd ask what would be the solution to overcome the problem
> > (apart from the desirable fixing the builders)?
> 
> Hi, I'm glad I (finally) got some response to the problem!
> 
> I've had precisely the same problem as Filippo: I prepared my first package, I
> spent many hours studying the Policy to follow it precisely, and to my
> disappointment, I got a FTBFS bug report immediately after uploading the
> package.

I suspected I was not alone in this situation :)

> I don't think the problem is so much in the Policy, I think the problem is 
> with
> the builders. The builders must provide dependencies according to
> debian/control and the target(s) they're calling. Of course, improving the
> Policy is OK, but once the guidelines are agreed upon and written there, the
> builders must follow it.

I agree with this, also because what is stated in Policy is just plain
sensible.

> Not the other way around.  I'm quite surprised that
> these problems with the builders haven't been solved already, considering the
> number of packages in Debian!

Well, maybe there are not so many packages that perform as a clear cut
separation between build-indep and build-arch...
 
> I suggest to create a dummy package that would be as simple as possible and
> that would demonstrate the problem. Then test it with various building tools 
> and
> fill eventual bug reports. Maybe I could prepare such dummy package in the
> following days, if I have time.

If this would convince the developers responsible for the builders to
deal with the problem, then that would be awsome. Any such DD
listening ?

Best regards,
 Filippo

--
Filippo Rusconi, PhD - CNRS - public key C78F687C
Author of ``massXpert'' at http://www.massxpert.org


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RFS: cb2bib

[Filippo Rusconi]

Dear mentor Debianists,

In accordance with my usual sponsor (Lionel Mamane) who is currently
rather busy, I am looking for a sponsor for my package "cb2bib" (First
Upload).

* Package name: cb2bib
  Version : 1.3.0-1
  Upstream Author : Pere Constans 
* URL : http://www.molspaces.com/cb2bib/
* License : GPL-3
  Section : text

It builds this single binary package:
cb2bib - extract bibliographic references from various sources

Some details to put you in appetite:

 cb2bib is a program to extract bibliographic references from
 unformatted and non standard sources, like:
  - email alerts;
  - journal Web pages;
  - and most interestingly PDF files. 
 .
 Output references are written to BibTeX-formatted files. Other
 features include:
  - article files can be linked and renamed by dragging them onto the
 cb2Bib window;
  - editing and browsing BibTeX files;
  - citing references, searching references and the full contents of
  the
 referenced documents;
  - inserting bibliographic metadata to documents;
  - writing short notes that interrelate several references.


The package appears to be lintian clean (unless for --pedantic
warnings about spelling errors in cb2bib binary that I already have
sent to upstream for correction in the next version).

The upload would fix this ITP bug: 529399

The package can be found on mentors.debian.net:
- URL: http://mentors.debian.net/debian/pool/main/c/cb2bib
- Source repository: deb-src http://mentors.debian.net/debian unstable
- main contrib non-free
- dget
- http://mentors.debian.net/debian/pool/main/c/cb2bib/cb2bib_1.3.0-1.dsc

I would be glad if someone 1) checked and 2) uploaded this package for
me.

Kind regards
 Filippo

-- 
Filippo Rusconi, PhD - CNRS - public key C78F687C
Author of ``massXpert'' at http://www.massxpert.org


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RFS: colorcode

[Filippo Rusconi]

Dear mentors,

I am looking for a sponsor for my package "colorcode".

* Package name: colorcode
  Version : 0.5.5-1
  Upstream Author : Dirk Laebisch 
* URL : http://colorcode.laebisch.com/
* License : GPL-3
  Section : games

It builds these binary packages:
colorcode  - advanced clone of the MasterMind code-breaking game

The package appears to be lintian clean.

The upload would fix these bugs: 553622

My motivation for maintaining this package is simply that this
implementation of the MasterMind code-breaking game is, in my opinion,
very good (and I've been looking for such a software since a pretty
long time).  I am using this program all the time and thus, I reason,
others might enjoy it in the Debian GNU/Linux distro.

The package can be found on mentors.debian.net:
- URL: http://mentors.debian.net/debian/pool/main/c/colorcode
- Source repository: deb-src http://mentors.debian.net/debian unstable
- main contrib non-free
- dget
- http://mentors.debian.net/debian/pool/main/c/colorcode/colorcode_0.5.5-1.dsc

I would be glad if someone uploaded this package for me.

Best regards,
     Filippo

-- 
Filippo Rusconi, PhD - CNRS - public key C78F687C
Author of ``massXpert'' at http://www.massxpert.org


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Re: RFS: colorcode

[Filippo Rusconi]

Hello, Lionel, 

thanks for caring :-)

On Sun, Nov 08, 2009 at 03:21:19PM +0100, Lionel Elie Mamane wrote:
> 
> On Thu, Nov 05, 2009 at 11:22:42PM +0100, Filippo Rusconi wrote:
> > I am looking for a sponsor for my package "colorcode".
> 
> > * Package name: colorcode
> >   Version : 0.5.5-1
> >   Upstream Author : Dirk Laebisch 
> > * URL : http://colorcode.laebisch.com/
> > * License : GPL-3
> >   Section : games
> 
> usr/share/pixmaps/colorcode32.xpm: neither gqview nor xli shows it
> reasonably. xli complains with error messages like
>  Bad color name '#A7ADAD00'

OK, this one is odd :

I installed xli for the test and it ran flawlessly (displaying the pixmap
as expected):

$ xli /usr/share/pixmaps/colorcode32.xpm
/usr/share/pixmaps/colorcode32.xpm is a 32x32 X Pixmap image (Version
3) with 229 colors titled 'colorcode__'
  Default gamma for IRGB image is  2.20
  Compressing colormap...212 unique colors
  Using DirectColor visual
  Building XImage...done

I also opened it using Gwenview and The Gimp (which is in my
experience picky about file formats) without any warning/error
message.

I wonder what this odd behaviour is due to. Note that this xpm file is
created on the fly by calling convert on a .ico file. Maybe the
conversion failed, somehow ? I am attaching the file so that you may
try it on your box.

> 
> debian/rules:
> 
>   - $(MAKE) clean
> 
> The space after "-" keeps lintian from detecting this, but
> 
> W: colorcode source: debian-rules-ignores-make-clean-error line 32
> N: 
> N:A rule in the debian/rules file for this package calls the package's
> N:clean or distclean target with a line like:
> N:
> N: -$(MAKE) distclean
> N:or
> N: $(MAKE) -i distclean
> N:
> N:The leading "-" or the option -i tells make to ignore all errors.
> N:Normally this is done for packages using Autoconf since Makefile may not
> N:exist. However, this line ignores all other error messages, not just the
> N:missing Makefile error. It's better to use:
> N:
> N: [ ! -f Makefile ] || $(MAKE) distclean
> N:
> N:so that other error messages from the clean or distclean rule will still
> N:be caught (or just remove the "-" if the package uses a static
> N:makefile).
> N:
> N:Severity: normal, Certainty: certain
> N: 

Thanks for this one. Fixed.

> Except for that, it looks OK.

Great !

Please, note that the lintian -iEI --pedantic run on the package
complains about the man page since one day (yesterday it did not
complain at all).

Apparently there is a bug in either col or man with respect to
character codes depending on the encoding of the man page. Please have
a look at http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=555330.

I am uploading the modified package.

Thanks again !

Ciao,
 Filippo

-- 
Filippo Rusconi, PhD - CNRS - public key C78F687C
Author of ``massXpert'' at http://www.massxpert.org
<>

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Re: auto editing changelog

[Filippo Rusconi]

Hello, bonjour, ciao :-)

On Thu, May 13, 2010 at 09:56:07PM +0300, Mihamina Rakotomandimby wrote:
> 
> Manao ahoana, Hello, Bonjour,
> 
> Into the debian/directory, there is the changelog file.
> I feel it heavy to get and format the date, then paste it in the file.
> 
> I mostly use Emacs when editing my package.
> 
> Is there an Emacs thing to do it automatically?

Great, then you simply can install the devscripts package (might be
installed already) which provides the useful dch program which you
typically invoke (while sitting in the top source directory
that contains the debian/ directory) using :

$ dch

This will open debian/changelog in emacs with an updated `date -R`
line.

$ man dch

for all the *many* options available to you.

Also note that you may want to install the dpkg-dev-el package, which
provides the debian-changelog mode to properly highlight the syntax of
the changelog file.

Happy hacking,

Best regards,
         Filippo

-- 
Filippo Rusconi, PhD - CNRS - public key C78F687C
Author of ``massXpert'' at http://www.massxpert.org


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Re: different version numbers?

[Filippo Rusconi]

Greetings,

On Mon, Jul 25, 2011 at 10:13:56PM -0500, Paul Elliott wrote:

> What is the relationship, if any, between the version number of the source 
> pachage and the version number of a library, which has to do with SONAME.
> 
> What do these have to do with PACKAGE_VERSION in autotools?
> 
> My up stream, has version number associated with his source tarballs,
> that have nothing to do with debian or Linux, because he does not develop
> with Linux in mind. All though he does build a Linux static library.

As library packaging is generally regarded as a difficult task, a very
good guide at

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

is a recommended reading. That guide contains also very clear
background information on the various version numbering systems
possibly involved.

Best regards,

Filippo

-- 
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Author of ``massXpert'' at http://www.massxpert.org


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Re: RE : different version numbers?

[Filippo Rusconi]

Greetings,

On Tue, Jul 26, 2011 at 08:26:19AM +, PICCA Frédéric-Emmanuel wrote:
> > As library packaging is generally regarded as a difficult task, a very
> > good guide at
> 
> > http://www.netfort.gr.jp/~dancer/column/libpkg-guide/libpkg-guide.html
> 
> > is a recommended reading. That guide contains also very clear
> > background information on the various version numbering systems
> > possibly involved.
> 
> Yes it is a good introduction, but I could not find an answer to
> that question:
> 
> libX + libX-dev
> 
> or
> 
> libX + lib-dev
> 
> 
> It is not clear to me what is the best practice.

It is my understanding that both are possible, depending on what the
packager wishes to actually package. The most general case is that the
packager only wants to package the developement files for the last
version of the library. In that case, lib-dev is fine, because each
time that package gets installed it "overwrites" the files shipped
with the previous version.

It might happen, however, that the packager wishes to support the
developement of various versions of the library. Because two same
files can not belong to two different simultaneousy installable
packages (that would be a conflict), then it is required that the
developement files for lib1 be packaged in lib1-dev and the
development files for lib2 be packaged in lib2-dev.

Hope this helps (and is actually a correct understanding of the -dev
package naming/numbering process),

Kind regards,
Filippo

-- 
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Author of ``massXpert'' at http://www.massxpert.org


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search of mentor for a scientific package

[Filippo Rusconi]

Hello,

this is mail is to enquire if somebody would help me as a mentor to
construct correct packages for a software suite (one arch indep
package, two libraries, three exec binaries). This software suite,
called GNU polyxmass, attempts to provide the scientist a set of
useful programs in the field of mass spectrometry of (bio)polymers.

The description, for the potential interested mentor, is located at 

www.gnu.org/software/polyxmass

Note that I've been developing this program under RedHat GNU/Linux,
but it's already two months or so that I have __very__ happily
switched to the Debian GNU/Linux distribution...

Cheers,

Filippo

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Thank you. 

Filippo Rusconi, PhD

Author-Maintainer of the *GNU polyxmass* project for a free mass
spectrometric computing environment


Mass spectrometry in GNU/Linux ? GNU polyxmass (TM) !

 www.gnu.org/software/polyxmass or www.polyxmass.org

  Free software that you are welcome to distribute!
   
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packages from a newbie Debian GNU/Linux fan

[Filippo Rusconi]

Hi all,

as suggested previously by one peer, I have tried my best preparing
Debian packages for the different libraries and modules from the GNU
polyxmass project. 

I seemed to be able to man (1)-answer all my questions during the
investigation of the Debian packaging procedures, but I cannot
guarantee that the packages are perfect (there are two libraries, as
shown below, and for these specific packages I may have not understood
everything right).

I have put everything on the following site:

http://polyxmass.org/debian-packages

The kind person, willing to inspect the packages may have them
installed in the following order:


dpkg -i polyxmassdata_0.6.4-1_all.deb

dpkg -i libpxmutils3_0.6.3-1_i386.deb  (-dev variant available)

dpkg -i libpxmchem4_0.6.4-1_i386.deb  (-dev variant available)

dpkg -i polyxdef_0.6.5-1_i386.deb

dpkg -i polyxcalc_0.6.5-1_i386.deb

dpkg -i polyxedit_0.6.6-1_i386.deb


The polyxmassdata_0.6.4-1_all.deb package should contain a pretty
detailed manual that should get installed in

/usr/share/doc/polyxmassdata/pdf/polyxmass.pdf

If these packages can successfully be installed, I'd be happy if
someone would sponsor them for inclusion in unstable (but that might
well be too soon).

Cheers,

Filippo


-- 

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GNU polyxmass: brand new lintian-linda-clean packages

[Filippo Rusconi]

Hi all,

Some days ago I asked if someone would help me assess if the packages
I prepared for the GNU polyxmass project were OK, and some kind soul
pointed me to some errors that were detected by lintian.

(This project is GPL'ed software, aimed at allowing user perform
simulations and analyzes of polymer mass spectrometric data.)

I've reworked the packages now and they are lintian-linda-clean unless
for two things:

1. the menu icon (that is limited to 24 colors using The Gimp) makes
   the verification programs complain about colors which are non
   correct. I could not find a solution to this problem and found on
   the web that lintian was buggy with this respect. Anyone ideas ?

2. the verification program also pretends that the detailed
   description might contain a non-indented section (control
   file). However, I could not find why there was this diagnostic.

Apart from those lintian W/E messages, the packages are clean.

I would be glad if someone was interested in that software, and would
try the packages that I made.

The packages should be apt-get'table from

deb http://www.polyxmass.org/debian-packages binary-i386/
deb-src http://www.polyxmass.org/debian-packages source/

I tried this with

# apt-get install polyxdef

and it correctly determined the dependencies on a virginal Debian
GNU/Linux machine, downloading everything needed (what a wonder !).

Overall, the fact that I had to prepare Debian packages certainly made
me improve the upstream material. That's clever, for a packaging
system!

Thanks for your help,

Bye,

--

Filippo

Mass spectrometry in GNU/Linux ? GNU polyxmass !

 www.gnu.org/software/polyxmass or www.polyxmass.org

  Free software that you are welcome to distribute!
   
  http://www.unesco.org/webworld/portal_freesoft/index.shtml



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what the number of colors message from lintian means

[Filippo Rusconi]

Hi all,

I'm trying to build really lintian clean packages for my software.

I have a menu icon that is 32x32 pixels, that I have indexed using The
Gimp, asking that it be made of 24 colors. When I package the software
I get the following error message:

E: polyxdef: menu-icon-has-bad-colors /usr/share/pixmaps/polyxdef.xpm:
#3E7F3E, #3F027F, #4A1682, #521E82, #5A2E82, #32, #744C80,
#7A5E86, #862E66, #927080, #A0383C, #A44A4C, #A65A6A, #B60230,
#B84652, #BE2A16, #C2022A, #C8363F, #CE1A2E, #D61A26, #DB242B,
#EA1416, #EC0710, #FD0303

OK, now I go back to The Gimp, and ask that the pixmap be of 15 colors
only. The error message above still shows up, albeit with less
hexadecimal numbers...

I've tried finding in the web for an answer to this question but all I
could find is a page that states that the lintian package is buggy
with respect to that pixmap check.

Could somebody help be with this problem, please ?

Thanks for any pointer,

Filippo

-- 

Mass spectrometry in GNU/Linux ? GNU polyxmass !

 www.gnu.org/software/polyxmass or www.polyxmass.org

  Free software that you are welcome to distribute!
   
  http://www.unesco.org/webworld/portal_freesoft/index.shtml


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problem with files in /etc/dir.d

[Filippo Rusconi]

Hello all,

in the software that I'm trying (gosh, that's not trivial...) to
package, some configuration files are due to go in /etc/polyxmass.d

For example, on file belonging to a "all type package, ie data-only"
should go like this:

/etc/polyxmass.d/polyxmassdata.conf

Now, when I try to package this, with the following rules' specifs 

~~ excerpt rules
# Build architecture-independent files here.
binary-indep: build install
dh_testdir
dh_testroot
dh_installchangelogs ChangeLog
dh_installdocs
dh_installman
# below: we do not want that the files in the userman directory
# be compressed (because they are located in .../doc/... directory).
dh_compress -Xuserman
dh_fixperms
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb

binary: binary-indep 
.PHONY: build clean binary-indep binary-arch binary install 
 end excerpt rules

I effectively get the said file in 

debian/polyxmassdata/etc/polyxmass.d/polyxmassdata.conf

telling me that the "make install" target has worked ok.

However, I also noticed that this file is referenced here:

debian/polyxmassdata/DEBIAN/conffiles

although I never had a conffiles for this package, because the
polyxmassdata.conf SHOULD be overwritten upon a new install.

The result of all this is that the polyxmassdata.conf seems to be
included in the deb file (as seen using "dpkg -X file.deb /tmp"), but
does not get installed (presumably because, indeed, the debian
packaging system does think it is a conffile).

So my question ? How can I have a configuration file installed
somewhere in /etc without having the debian packaging system think it
is a conffile ?

Thanks for reading up to here,

any help appreciated !

Cheers,

Filippo

-- 

Mass spectrometry in GNU/Linux ? GNU polyxmass !

 www.gnu.org/software/polyxmass or www.polyxmass.org

  Free software that you are welcome to distribute!
   
  http://www.unesco.org/webworld/portal_freesoft/index.shtml


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Description: Digital signature

problem with files in /etc/dir.d (continued)

[Filippo Rusconi]

Hello,

Thanks to the persons who have kindly answered my questions about the
/etc/dir.d/ problem.

At the beginning, the software did use the /usr/etc/dir.d
configuration directory, but then the packaging system would complain
that this is not a standard location. I used this location because
that is simpler, using the ${prefix}-based variables from the
autotools (that is : ${sysconfdir} will resolve to /usr/etc if
${prefix} is /usr).

So, if it is not correct to put the stuff in /usr/etc (can someone
help me decide if this is actually forbidden ?), I'll put the conf
files in a /usr/share/thepackage/dir.d directory. 

In fact, I seem to understand that /usr/etc is forbidden by the
standards. However, then, why do the autotools provide a ${sysconfdir}
variable that resolves to /usr/etc if ${prefix} is /usr ?.

Thanks so much for your help,

Cheers,

Filippo

-- 
Mass spectrometry in GNU/Linux ? GNU polyxmass !

 www.gnu.org/software/polyxmass or www.polyxmass.org

  Free software that you are welcome to distribute!
   
  http://www.unesco.org/webworld/portal_freesoft/index.shtml


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search for a sponsor

[Filippo Rusconi]

Hi everybody,

after some studying/learning/suffering I finally got to package the
different modules of the GNU polyxmass project.

These packages are lintian/linda clean (except for the bad-colors
error that I could not succeed to remove, even by following
indications from this list members).

I could install all the packages in the software project using apt-get
with the following two lines in sources.list:

deb http://www.polyxmass.org/debian-packages binary-i386/
deb-src http://www.polyxmass.org/debian-packages source/

I hope somebody will be interested in this scientific package of which
a description is available at http://www.polyxmass.org.

Briefly, mass spectrometry is a very powerful analytical technique
that allows the measurement of molecular weights of molecules. Knowing
the molecular mass of a molecule is the first crucial step in the
analytical process that leads to the determination of that molecule's
structure. Mass spectrometry is incredibly popular these days, as it
is the founding technique of new biological fiels, like proteomics and
systems biology. 

GNU polyxmass aims at giving to the user the ability to
simulate/predict and analyze mass spectrometric data obtained on
polymeric molecules. What sets this program apart, as a unique mass
spectrometry software project is that the user is able to define brand
new polymer chemistries (polyxdef module). The polymer chemistry
definition files (XML-format) are then made available to the other
modules: a mass calculator (usable as a desktop calculator) and a
hyper-powerful polymer sequence editor and chemistry simulator
(polyxedit).

I hope that somebody will want to check that software suite. Note that
a whishlist bug gets closed with these packages, and I have received
already a number of encouraging messages from user who either use the
program already or who are happy that it could become part of the
Debian GNU/Linux distribution.

Cheers,

Filippo

-- 
Mass spectrometry in GNU/Linux ? GNU polyxmass !

 www.gnu.org/software/polyxmass or www.polyxmass.org

  Free software that you are welcome to distribute!
   
  http://www.unesco.org/webworld/portal_freesoft/index.shtml


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search of mentor for a scientific package

[Filippo Rusconi]

Hello,

this is mail is to enquire if somebody would help me as a mentor to
construct correct packages for a software suite (one arch indep
package, two libraries, three exec binaries). This software suite,
called GNU polyxmass, attempts to provide the scientist a set of
useful programs in the field of mass spectrometry of (bio)polymers.

The description, for the potential interested mentor, is located at 

www.gnu.org/software/polyxmass

Note that I've been developing this program under RedHat GNU/Linux,
but it's already two months or so that I have __very__ happily
switched to the Debian GNU/Linux distribution...

Cheers,

Filippo

-- 
HTML-only mail goes to trash. Use simple text mail for me. 
Thank you. 

Filippo Rusconi, PhD

Author-Maintainer of the *GNU polyxmass* project for a free mass
spectrometric computing environment


Mass spectrometry in GNU/Linux ? GNU polyxmass (TM) !

 www.gnu.org/software/polyxmass or www.polyxmass.org

  Free software that you are welcome to distribute!
   
  http://www.unesco.org/webworld/portal_freesoft/index.shtml


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packages from a newbie Debian GNU/Linux fan

[Filippo Rusconi]

Hi all,

as suggested previously by one peer, I have tried my best preparing
Debian packages for the different libraries and modules from the GNU
polyxmass project. 

I seemed to be able to man (1)-answer all my questions during the
investigation of the Debian packaging procedures, but I cannot
guarantee that the packages are perfect (there are two libraries, as
shown below, and for these specific packages I may have not understood
everything right).

I have put everything on the following site:

http://polyxmass.org/debian-packages

The kind person, willing to inspect the packages may have them
installed in the following order:


dpkg -i polyxmassdata_0.6.4-1_all.deb

dpkg -i libpxmutils3_0.6.3-1_i386.deb  (-dev variant available)

dpkg -i libpxmchem4_0.6.4-1_i386.deb  (-dev variant available)

dpkg -i polyxdef_0.6.5-1_i386.deb

dpkg -i polyxcalc_0.6.5-1_i386.deb

dpkg -i polyxedit_0.6.6-1_i386.deb


The polyxmassdata_0.6.4-1_all.deb package should contain a pretty
detailed manual that should get installed in

/usr/share/doc/polyxmassdata/pdf/polyxmass.pdf

If these packages can successfully be installed, I'd be happy if
someone would sponsor them for inclusion in unstable (but that might
well be too soon).

Cheers,

Filippo


-- 

http://www.polyxmass.org/varia/filippo-rusconi-gnupg-public-key.asc

Author-Maintainer of the *GNU polyxmass* project for a free mass
spectrometric computing environment



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GNU polyxmass: brand new lintian-linda-clean packages

[Filippo Rusconi]

Hi all,

Some days ago I asked if someone would help me assess if the packages
I prepared for the GNU polyxmass project were OK, and some kind soul
pointed me to some errors that were detected by lintian.

(This project is GPL'ed software, aimed at allowing user perform
simulations and analyzes of polymer mass spectrometric data.)

I've reworked the packages now and they are lintian-linda-clean unless
for two things:

1. the menu icon (that is limited to 24 colors using The Gimp) makes
   the verification programs complain about colors which are non
   correct. I could not find a solution to this problem and found on
   the web that lintian was buggy with this respect. Anyone ideas ?

2. the verification program also pretends that the detailed
   description might contain a non-indented section (control
   file). However, I could not find why there was this diagnostic.

Apart from those lintian W/E messages, the packages are clean.

I would be glad if someone was interested in that software, and would
try the packages that I made.

The packages should be apt-get'table from

deb http://www.polyxmass.org/debian-packages binary-i386/
deb-src http://www.polyxmass.org/debian-packages source/

I tried this with

# apt-get install polyxdef

and it correctly determined the dependencies on a virginal Debian
GNU/Linux machine, downloading everything needed (what a wonder !).

Overall, the fact that I had to prepare Debian packages certainly made
me improve the upstream material. That's clever, for a packaging
system!

Thanks for your help,

Bye,

--

Filippo

Mass spectrometry in GNU/Linux ? GNU polyxmass !

 www.gnu.org/software/polyxmass or www.polyxmass.org

  Free software that you are welcome to distribute!
   
  http://www.unesco.org/webworld/portal_freesoft/index.shtml



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Description: Digital signature

what the number of colors message from lintian means

[Filippo Rusconi]

Hi all,

I'm trying to build really lintian clean packages for my software.

I have a menu icon that is 32x32 pixels, that I have indexed using The
Gimp, asking that it be made of 24 colors. When I package the software
I get the following error message:

E: polyxdef: menu-icon-has-bad-colors /usr/share/pixmaps/polyxdef.xpm:
#3E7F3E, #3F027F, #4A1682, #521E82, #5A2E82, #32, #744C80,
#7A5E86, #862E66, #927080, #A0383C, #A44A4C, #A65A6A, #B60230,
#B84652, #BE2A16, #C2022A, #C8363F, #CE1A2E, #D61A26, #DB242B,
#EA1416, #EC0710, #FD0303

OK, now I go back to The Gimp, and ask that the pixmap be of 15 colors
only. The error message above still shows up, albeit with less
hexadecimal numbers...

I've tried finding in the web for an answer to this question but all I
could find is a page that states that the lintian package is buggy
with respect to that pixmap check.

Could somebody help be with this problem, please ?

Thanks for any pointer,

Filippo

-- 

Mass spectrometry in GNU/Linux ? GNU polyxmass !

 www.gnu.org/software/polyxmass or www.polyxmass.org

  Free software that you are welcome to distribute!
   
  http://www.unesco.org/webworld/portal_freesoft/index.shtml


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Description: Digital signature

problem with files in /etc/dir.d

[Filippo Rusconi]

Hello all,

in the software that I'm trying (gosh, that's not trivial...) to
package, some configuration files are due to go in /etc/polyxmass.d

For example, on file belonging to a "all type package, ie data-only"
should go like this:

/etc/polyxmass.d/polyxmassdata.conf

Now, when I try to package this, with the following rules' specifs 

~~ excerpt rules
# Build architecture-independent files here.
binary-indep: build install
dh_testdir
dh_testroot
dh_installchangelogs ChangeLog
dh_installdocs
dh_installman
# below: we do not want that the files in the userman directory
# be compressed (because they are located in .../doc/... directory).
dh_compress -Xuserman
dh_fixperms
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb

binary: binary-indep 
.PHONY: build clean binary-indep binary-arch binary install 
 end excerpt rules

I effectively get the said file in 

debian/polyxmassdata/etc/polyxmass.d/polyxmassdata.conf

telling me that the "make install" target has worked ok.

However, I also noticed that this file is referenced here:

debian/polyxmassdata/DEBIAN/conffiles

although I never had a conffiles for this package, because the
polyxmassdata.conf SHOULD be overwritten upon a new install.

The result of all this is that the polyxmassdata.conf seems to be
included in the deb file (as seen using "dpkg -X file.deb /tmp"), but
does not get installed (presumably because, indeed, the debian
packaging system does think it is a conffile).

So my question ? How can I have a configuration file installed
somewhere in /etc without having the debian packaging system think it
is a conffile ?

Thanks for reading up to here,

any help appreciated !

Cheers,

Filippo

-- 

Mass spectrometry in GNU/Linux ? GNU polyxmass !

 www.gnu.org/software/polyxmass or www.polyxmass.org

  Free software that you are welcome to distribute!
   
  http://www.unesco.org/webworld/portal_freesoft/index.shtml


signature.asc
Description: Digital signature

problem with files in /etc/dir.d (continued)

[Filippo Rusconi]

Hello,

Thanks to the persons who have kindly answered my questions about the
/etc/dir.d/ problem.

At the beginning, the software did use the /usr/etc/dir.d
configuration directory, but then the packaging system would complain
that this is not a standard location. I used this location because
that is simpler, using the ${prefix}-based variables from the
autotools (that is : ${sysconfdir} will resolve to /usr/etc if
${prefix} is /usr).

So, if it is not correct to put the stuff in /usr/etc (can someone
help me decide if this is actually forbidden ?), I'll put the conf
files in a /usr/share/thepackage/dir.d directory. 

In fact, I seem to understand that /usr/etc is forbidden by the
standards. However, then, why do the autotools provide a ${sysconfdir}
variable that resolves to /usr/etc if ${prefix} is /usr ?.

Thanks so much for your help,

Cheers,

Filippo

-- 
Mass spectrometry in GNU/Linux ? GNU polyxmass !

 www.gnu.org/software/polyxmass or www.polyxmass.org

  Free software that you are welcome to distribute!
   
  http://www.unesco.org/webworld/portal_freesoft/index.shtml


signature.asc
Description: Digital signature

search for a sponsor

[Filippo Rusconi]

Hi everybody,

after some studying/learning/suffering I finally got to package the
different modules of the GNU polyxmass project.

These packages are lintian/linda clean (except for the bad-colors
error that I could not succeed to remove, even by following
indications from this list members).

I could install all the packages in the software project using apt-get
with the following two lines in sources.list:

deb http://www.polyxmass.org/debian-packages binary-i386/
deb-src http://www.polyxmass.org/debian-packages source/

I hope somebody will be interested in this scientific package of which
a description is available at http://www.polyxmass.org.

Briefly, mass spectrometry is a very powerful analytical technique
that allows the measurement of molecular weights of molecules. Knowing
the molecular mass of a molecule is the first crucial step in the
analytical process that leads to the determination of that molecule's
structure. Mass spectrometry is incredibly popular these days, as it
is the founding technique of new biological fiels, like proteomics and
systems biology. 

GNU polyxmass aims at giving to the user the ability to
simulate/predict and analyze mass spectrometric data obtained on
polymeric molecules. What sets this program apart, as a unique mass
spectrometry software project is that the user is able to define brand
new polymer chemistries (polyxdef module). The polymer chemistry
definition files (XML-format) are then made available to the other
modules: a mass calculator (usable as a desktop calculator) and a
hyper-powerful polymer sequence editor and chemistry simulator
(polyxedit).

I hope that somebody will want to check that software suite. Note that
a whishlist bug gets closed with these packages, and I have received
already a number of encouraging messages from user who either use the
program already or who are happy that it could become part of the
Debian GNU/Linux distribution.

Cheers,

Filippo

-- 
Mass spectrometry in GNU/Linux ? GNU polyxmass !

 www.gnu.org/software/polyxmass or www.polyxmass.org

  Free software that you are welcome to distribute!
   
  http://www.unesco.org/webworld/portal_freesoft/index.shtml


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