Bug#669598: RFS: python-django-djblets/0.6.17-1 [ITP] -- Collection of useful extensions for Django

2012-04-22 Thread Dmitry Nezhevenko
On Sun, Apr 22, 2012 at 12:43:42PM +0200, Holger Levsen wrote:
> Hi Dmitry,
> 
> On Freitag, 20. April 2012, Dmitry Nezhevenko wrote:
> > dget -x
> > http://mentors.debian.net/debian/pool/main/p/python-django-djblets/python-d
> > jango-djblets_0.6.17-1.dsc
> 
> a quick review reveals that you modified the upstream orig.tar.gz, yet you 
> don't document this (and why). Please either document this or do'nt do it.

Oops. Yes. It was done initially (actually converted from downloaded zip
at github). There are no actual changes to upstream sources except that.
Anyway I've switched to upstream tarball for it and md5 for orig.tar.gz
matches to upstream:


http://downloads.reviewboard.org/releases/Djblets/0.6/Djblets-0.6.17.tar.gz

I've uploaded fixed pkg to mentors:

dget -x 
http://mentors.debian.net/debian/pool/main/p/python-django-djblets/python-django-djblets_0.6.17-1.dsc

Thanks

-- 
WBR, Dmitry


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Bug#669598: RFS: python-django-djblets/0.6.17-1 [ITP] -- Collection of useful extensions for Django

2012-04-22 Thread Holger Levsen
Hi Dmitry,

On Freitag, 20. April 2012, Dmitry Nezhevenko wrote:
> dget -x
> http://mentors.debian.net/debian/pool/main/p/python-django-djblets/python-d
> jango-djblets_0.6.17-1.dsc

a quick review reveals that you modified the upstream orig.tar.gz, yet you 
don't document this (and why). Please either document this or do'nt do it.


cheers,
Holger



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Bug#669598: RFS: python-django-djblets/0.6.17-1 [ITP] -- Collection of useful extensions for Django

2012-04-22 Thread Holger Levsen
Hi,

On Sonntag, 22. April 2012, Dmitry Nezhevenko wrote:
> Oops. Yes. It was done initially (actually converted from downloaded zip
> at github). There are no actual changes to upstream sources except that.
> Anyway I've switched to upstream tarball for it and md5 for orig.tar.gz
> matches to upstream:

thanks! (+confirmed :)


cheers,
Holger



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Bug#669722: RFS: gnunet/0.9.2-1 [ITA]

2012-04-22 Thread Christoph Egger
Hi!

Bertrand Marc  writes:
> I am looking for a sponsor for my package "gnunet"
>
> * Package name: gnunet
>   Version : 0.9.2-1
>   Upstream Author : Christian Grothoff 
> * URL : https://gnunet.org
> * License : GPL3
>   Section : net
>
> It builds those binary packages:
>
>  gnunet - secure, trust-based peer-to-peer framework (meta)
>  gnunet-client - secure, trust-based peer-to-peer framework (client)
>  gnunet-common - secure, trust-based peer-to-peer framework (common)
>  gnunet-dbg - secure, trust-based peer-to-peer framework (debug)
>  gnunet-dev - secure, trust-based peer-to-peer framework (development)
>  gnunet-server - secure, trust-based peer-to-peer framework (server)
>
>  To access further information about this package, please visit the
> following URL:
>
>  http://mentors.debian.net/package/gnunet
>
> Alternatively, one can download the package with dget using this command:
>
> dget -x 
> http://mentors.debian.net/debian/pool/main/g/gnunet/gnunet_0.9.2-1.dsc

==

uscan warning: In debian/watch no matching files for watch line
  ftp://ftp.gnu.org/gnu/gnunet/gnunet-(\d.+).tar.gz

==

The dependency on libmicrohttpd-dev can only be fullfilled in
experimental while you're trying to upload to unstable?

==

FTBFS:

configure: error: GNUnet requires libextractor

==

dpkg-source: info: local changes detected, the modified files are:
 /home/christoph/code/debian/sponsoring/gnunet-0.9.2/config.log
dpkg-source: info: you can integrate the local changes with dpkg-source --commit

==

Regards

Christoph

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Re: Packaging where upstream only has a git repo

2012-04-22 Thread Henrique de Moraes Holschuh
On Sun, 22 Apr 2012, Michael van der Kolff wrote:
> Never mind, I found a real upstream.  Turned out the author moved
> development from github, but left no pointer :(

Write to him, introducing yourself as a downstream maintainer, and also tell
him the lack of a "forwarding address" in github is causing problems.

-- 
  "One disk to rule them all, One disk to find them. One disk to bring
  them all and in the darkness grind them. In the Land of Redmond
  where the shadows lie." -- The Silicon Valley Tarot
  Henrique Holschuh


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Bug#669722: RFS: gnunet/0.9.2-1 [ITA]

2012-04-22 Thread Helmut Grohne
Thanks for your work on the gnunet package.

On Sat, Apr 21, 2012 at 01:11:29PM +0200, Bertrand Marc wrote:
> dget -x http://mentors.debian.net/debian/pool/main/g/gnunet/gnunet_0.9.2-1.dsc

Why does the -dbg package depend on all other packages? Wouldn't it be
enough to depend on -common since all other packages (indirectly) depend
on -common?

Your copyright file uses something close to dep5. Now that dep5 is
finalized, could you add a format specification?

The (upstream) AUTHORS file lists a large number of contributors, but
debian/copyright only states a few of them. Maybe you could refer to the
AUTHORS file in a "Comment" paragraph?

Maybe you could also have a closer look at the individual files. For
instance po/sv.po lists the FSF as copyright owner. Also
src/include/plibc.h lists Nils Durner as copyright owner. And finally
debian/po/*.po list a number of other copyright owners.

Did you consider using dpkg-statoverride instead of chown to set up the
setuid binaries? That would allow an administrator to revoke certain
privileges (such as -transport-wlan on a system without wlan).

Also please be explicit about which binaries to chmod 4754. Certainly no
other package should create any /usr/bin/gnunet-helper-nat-foo, but if
it does things go badly wrong.

gnunet-server purge does not use debconf to determine which groups and
user to delete, but always deletes gnunet and gnunetdns even though I
might have changed them in postinst.

Since all packages (except gnunet-server) contain the very same
documentation and all packages (indirectly) depend on gnunet-common, you
could use dh_installdocs --link-doc and install the two READMEs for
gnunet-server to gnunet-common while still saving space.

Hope this helps

Helmut



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Re: Modifications of the changelog.

2012-04-22 Thread Bernhard R. Link
* Arno Töll  [120421 11:51]:
> The whole point of a changelog is a time dependent frozen point of view
> at your package. Once you released a version of a package, you should
> consider it untouchable

I strongly disagree. First of all, a changelog is there to see what has
changed when, i.e. it is a documentation of what important changed where
done and when (i.e. which package version) they were done for.
There is normally no reason to change older entries as most details get
less important over time, but if there is anything importing misleading
in them, something important incorrect or something important enough
missing, then not correcting the changelog is not acceptable in my eyes.

The new changelog should be about what was changed since the version
before (that might be some hint that the older changelog was corrected
if you prefer), but import changes in the old package should be in the
part of the changelog for the old package.

> as it would confuse people _a lot_ if you force
> them to read a full backlog of changes every time they upgrade because
> you /could/ have modified more than the latest entry.

Exactly the opposite is true in my opinion: If you already have the last
package, then the new changelog entry should only contain the changes
since then. But if you forgot to mention an important enough change in
an older version, and so not advertise that change there, then people
might use the wrong version because they get the wrong picture of where
which change was done. (When considering switching from package version
A to version B, it should be enough to read the the changelog entries
> A and <= B).

> Generally speaking it may be ok-ish in important cases to change
> previous entry if you restrict yourself to spelling fixes and formating
> changes, but it is completely unacceptable [to me, at least] to
> reformulate entries, add entries, remove entries and such.

If an old entry contains wrong information (either things claimed that
are not true, or changes missing that might be important, or
worded in a way that people to misunderstand) that is about things
important enough that a user could be mislead, I'd rather
consider it unacceptable to keep the wrong claims or omissions there.

There are of course several reason why not modifying old changelogs or
rather erring towards not changing it when being unsure is a good idea:

- the changelog format attributes each part of a changelog to a person.
  So modifying them should make sure one does not misrepresent those
  changes to changelog. (and if a change is small enough that making
  that clear would make it harder to read usually means it was not
  important enough to change it anyway).

- any change can introduce new bugs, even in documentation. If the
  changelog was from someone else (or from yourself from long enough
  ago), one should be sure enough about what one does.

(For the thing triggering this whole discussion: That appears to be
simply some needless contentless change in a NMU not related to the NMU,
so is quite unrelated to the "is editing old changelogs acceptable"
discussion.)

Bernhard R. Link


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Bug#670064: RFS: dylandotnet/11.2.9.2-1 [ITP] -- dylandotnet compiler

2012-04-22 Thread Dylan Borg
Package: sponsorship-requests
Severity: wishlist

Dear mentors,

  I am looking for a sponsor for my package "dylandotnet"

 * Package name: dylandotnet
   Version : 11.2.9.2-1
   Upstream Author : Dylan Borg 
 * URL : http://launchpad.net/dylandotnet
 * License : LGPL+3
   Section : cli-mono

  It builds those binary packages:

dylandotnet - This is the dylan.NET compiler for CLI 2.0.
dylandotnet-dev - These are the dylan.NET development tools.
dylandotnet-doc - This is the dylan.NET documentation.
dylandotnet4 - This is the dylan.NET compiler for CLI 4.0.

  To access further information about this package, please visit the following 
URL:

  http://mentors.debian.net/package/dylandotnet


  Alternatively, one can download the package with dget using this command:

dget -x 
http://mentors.debian.net/debian/pool/main/d/dylandotnet/dylandotnet_11.2.9.2-1.dsc

  More information about hello can be obtained from http://www.example.com.

  Changes since the last upload:

  dylandotnet (11.2.9.2-1) experimental; urgency=low
  
* (Closes:626078)
  
   -- Dylan Borg   Sun, 21 Apr 2012 18:57:04 +0100


  Regards,
   Dylan Borg

-- System Information:
Debian Release: wheezy/sid
  APT prefers precise-updates
  APT policy: (500, 'precise-updates'), (500, 'precise-security'), (500, 
'precise-proposed'), (500, 'precise'), (100, 'precise-backports')
Architecture: i386 (i686)

Kernel: Linux 3.2.0-23-generic-pae (SMP w/8 CPU cores)
Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8)
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Re: Modifications of the changelog.

2012-04-22 Thread Tomasz Muras

On 04/22/2012 02:48 PM, Bernhard R. Link wrote:

* Arno Töll  [120421 11:51]:

The whole point of a changelog is a time dependent frozen point of view
at your package. Once you released a version of a package, you should
consider it untouchable


I strongly disagree. First of all, a changelog is there to see what has
changed when, i.e. it is a documentation of what important changed where
done and when (i.e. which package version) they were done for.
There is normally no reason to change older entries as most details get
less important over time, but if there is anything importing misleading
in them, something important incorrect or something important enough
missing, then not correcting the changelog is not acceptable in my eyes.

The new changelog should be about what was changed since the version
before (that might be some hint that the older changelog was corrected
if you prefer), but import changes in the old package should be in the
part of the changelog for the old package.


I fully agree with Bernhard - basically if there is a good reason to 
improve old changelog entry, you should do it.
The idea of "freezing in time" and possibility to refer to an old, exact 
version of changelog (or any other file) looks like to job for Version 
Control software.


Tomek


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Help needed to fix g++ 4.7 error [Was: Bug#667120: bowtie: ftbfs with GCC-4.7]

2012-04-22 Thread Andreas Tille
Hi,

similarly to the plink case I can not found an easy solution for this
problem.

Kind regards

   Andreas.

- Forwarded message from Matthias Klose  -

Date: Tue, 03 Apr 2012 23:08:03 +
From: Matthias Klose 
To: mainto...@bugs.debian.org
Subject: Bug#667120: bowtie: ftbfs with GCC-4.7
X-Debian-PR-Message: report 667120
X-Debian-PR-Package: bowtie
X-Debian-PR-Keywords: sid wheezy
X-Debian-PR-Source: bowtie

Package: bowtie
Version: 0.12.7-1
Severity: important
Tags: sid wheezy
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-4.7

The package fails to build in a test rebuild on at least amd64 with
gcc-4.7/g++-4.7, but succeeds to build with gcc-4.6/g++-4.6. The
severity of this report may be raised before the wheezy release.

alphabet.h:48:3: error: 'reverseInPlace' was not declared in this scope, and no 
declarations were found by argument-dependent lookup at the point of 
instantiation [-fpermissive]

The full build log can be found at:
http://people.debian.org/~lucas/logs/2012/03/29-clang-gcc47/unstable-gcc47/bowtie_0.12.7-1_unstable-gcc47.log
The last lines of the build log are at the end of this report.

Some hints on fixing these issues can be found at
http://gcc.gnu.org/gcc-4.7/porting_to.html

To build with GCC 4.7, either set CC=gcc-4.7 CXX=g++-4.7 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

[...]
In file included from ebwt.h:24:0,
 from ebwt_build.cpp:11:
alphabet.h: In instantiation of 'void reverseComplementInPlace(TStr&, bool) 
[with TStr = seqan::String, 
seqan::Alloc >]':
hit.h:97:45:   required from here
alphabet.h:48:3: error: 'reverseInPlace' was not declared in this scope, and no 
declarations were found by argument-dependent lookup at the point of 
instantiation [-fpermissive]
alphabet.h:74:20: note: 'template void reverseInPlace(TStr&)' 
declared here, later in the translation unit
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
 from SeqAn-1.1/seqan/index.h:27,
 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct 
seqan::_PackedConsts, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:906:131:   required from 'typename 
seqan::Position > 
>::Type seqan::position(const seqan::Iter 
>&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename 
seqan::Position > 
>::Type = long unsigned int]'
SeqAn-1.1/seqan/sequence/string_packed.h:1237:40:   required from 'typename 
seqan::Difference > >::Type 
seqan::operator-(const seqan::Iter >&, 
const seqan::Iter >&) [with TContainer = 
const seqan::String, 
seqan::Packed<> >; THostspec = seqan::Alloc; typename 
seqan::Difference > >::Type = 
long int]'
SeqAn-1.1/seqan/sequence/string_base.h:181:51:   required from 'typename 
seqan::Size >::Type seqan::length(const 
seqan::String&) [with TValue = seqan::SimpleType; TSpec = seqan::Packed<>; typename seqan::Size >::Type = long unsigned int]'
blockwise_sa.h:354:32:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:291:2: warning: comparison between 
'enum seqan::BitsPerValue 
>::' and 'enum seqan::BitsPerValue::' 
[-Wenum-compare]
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct 
seqan::_PackedConsts, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:731:94:   required from 'typename 
seqan::Size > >::Type 
seqan::reserve(seqan::String >&, _TSize, 
seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Alloc; _TSize = long unsigned int; TExpand = 
seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]'
ebwt.h:3891:2:   required from 'static TStr 
Ebwt::join(std::vector&, std::vector&, uint32_t, 
const RefReadInParams&, uint32_t) [with TStr = 
seqan::String, seqan::Packed<> >; 
uint32_t = unsigned int]'
ebwt_build.cpp:463:9:   required from 'void driver(const string&, 
std::vector >&, const string&, bool) [with TStr = 
seqan::String, seqan::Packed<> >; 
std::string = std::basic_string]'
ebwt_build.cpp:600:69:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:291:2: warning: comparison between 
'enum seqan::BitsPerValue 
>::' and 'enum seqan::BitsPerValue::' 
[-Wenum-compare]
ref_read.cpp: In function 'void reverseRefRecords(const 
std::vector&, std::vector&, bool, bool)':
ref_read.cpp:195:8: warning: variable 'mergedLast' set but not used 
[-Wunused-but-set-variable]
ref_read.cpp: In function 'std::pair 
fastaRefReadSizes(std::vector&, std::vector&, 
std::vector&, const RefReadInParams&, BitpairOutFileBuf*, int&)':
ref_read.cpp:243:18: warning: variable 'rpcp' set but not used 
[-Wunused-but-set-variable]
make[2]: *** [bowtie-build] Error 1
make[2]: Leaving directory `/??PKGBUILDDIR??'
make[1]: *** [override_dh_auto_build] Error 2
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2




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Help needed [Was: Bug#667325: plink: ftbfs with GCC-4.7]

2012-04-22 Thread Andreas Tille
Hi,

I tried to follow the hints to fix this problem but failed.
Any more skilled C++ programmer than me who might have a clue?

Kind regards

 Andreas.

- Forwarded message from Matthias Klose  -

Date: Tue, 03 Apr 2012 23:11:40 +
From: Matthias Klose 
To: mainto...@bugs.debian.org
Subject: Bug#667325: plink: ftbfs with GCC-4.7
X-Debian-PR-Message: report 667325
X-Debian-PR-Package: plink
X-Debian-PR-Keywords: sid wheezy
X-Debian-PR-Source: plink

Package: plink
Version: 1.07-1
Severity: important
Tags: sid wheezy
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-4.7

The package fails to build in a test rebuild on at least amd64 with
gcc-4.7/g++-4.7, but succeeds to build with gcc-4.6/g++-4.6. The
severity of this report may be raised before the wheezy release.

sets.cpp:771:37: error: redeclaration of 'std::vector::iterator i'

The full build log can be found at:
http://people.debian.org/~lucas/logs/2012/03/29-clang-gcc47/unstable-gcc47/plink_1.07-1_unstable-gcc47.log
The last lines of the build log are at the end of this report.

Some hints on fixing these issues can be found at
http://gcc.gnu.org/gcc-4.7/porting_to.html

To build with GCC 4.7, either set CC=gcc-4.7 CXX=g++-4.7 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

[...]
sets.cpp:317:30: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp:323:40: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp:329:40: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp:332:39: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp:367:34: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp:370:37: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp: In member function 'void Set::initialiseSetMapping()':
sets.cpp:412:30: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp:413:38: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp: In member function 'void Set::empiricalSetPValues()':
sets.cpp:618:36: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp:619:34: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp:631:34: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp:632:32: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp:642:34: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp:643:32: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp: In member function 'vector_t Set::profileTestScore()':
sets.cpp:703:31: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp:713:43: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp:771:37: error: redeclaration of 'std::vector::iterator i'
sets.cpp:703:12: error: 'int i' previously declared here
sets.cpp: In member function 'vector_t Set::fitLDSetTest(vector_t&, bool)':
sets.cpp:905:31: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp:975:34: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
sets.cpp: In member function 'vector_t Set::fitStepwiseModel()':
sets.cpp:1042:31: warning: comparison between signed and unsigned integer 
expressions [-Wsign-compare]
make[1]: *** [sets.o] Error 1
make[1]: Leaving directory `/??PKGBUILDDIR??'
make: *** [build-stamp] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2




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Re: Help needed to fix g++ 4.7 error [Was: Bug#667120: bowtie: ftbfs with GCC-4.7]

2012-04-22 Thread Rodolfo García Peñas
On Sun, 22 Apr 2012, Andreas Tille escribió:

> Hi,
> 
> similarly to the plink case I can not found an easy solution for this
> problem.
> 
> Kind regards

I didn't have gcc 4.7, therefore I don't have the problem. IMO the problem is 
that the function "reverseInPlace" is declared after the function is used.

Is defined at line 74, but used at 48.

Probably the easiest solution is moving the block:

/// Reverse a string in-place
template 
static inline void reverseInPlace(TStr& s) {
typedef typename Value::Type TVal;
size_t len = length(s);
for(size_t i = 0; i < (len>>1); i++) {
TVal tmp = s[i];
s[i] = s[len-i-1];
s[len-i-1] = tmp;
}
}

before the function reverseComplementInPlace or create a function prototype 
(before the line 48 too):

template 
static inline void reverseInPlace(TStr& s);

I hope this helps.

Saludos,
kix
 
>Andreas.
> 
> - Forwarded message from Matthias Klose  -
> 
> Date: Tue, 03 Apr 2012 23:08:03 +
> From: Matthias Klose 
> To: mainto...@bugs.debian.org
> Subject: Bug#667120: bowtie: ftbfs with GCC-4.7
> X-Debian-PR-Message: report 667120
> X-Debian-PR-Package: bowtie
> X-Debian-PR-Keywords: sid wheezy
> X-Debian-PR-Source: bowtie
> 
> Package: bowtie
> Version: 0.12.7-1
> Severity: important
> Tags: sid wheezy
> User: debian-...@lists.debian.org
> Usertags: ftbfs-gcc-4.7
> 
> The package fails to build in a test rebuild on at least amd64 with
> gcc-4.7/g++-4.7, but succeeds to build with gcc-4.6/g++-4.6. The
> severity of this report may be raised before the wheezy release.
> 
> alphabet.h:48:3: error: 'reverseInPlace' was not declared in this scope, and 
> no declarations were found by argument-dependent lookup at the point of 
> instantiation [-fpermissive]
> 
> The full build log can be found at:
> http://people.debian.org/~lucas/logs/2012/03/29-clang-gcc47/unstable-gcc47/bowtie_0.12.7-1_unstable-gcc47.log
> The last lines of the build log are at the end of this report.
> 
> Some hints on fixing these issues can be found at
> http://gcc.gnu.org/gcc-4.7/porting_to.html
> 
> To build with GCC 4.7, either set CC=gcc-4.7 CXX=g++-4.7 explicitly,
> or install the gcc, g++, gfortran, ... packages from experimental.
> 
> [...]
> In file included from ebwt.h:24:0,
>  from ebwt_build.cpp:11:
> alphabet.h: In instantiation of 'void reverseComplementInPlace(TStr&, bool) 
> [with TStr = seqan::String, 
> seqan::Alloc >]':
> hit.h:97:45:   required from here
> alphabet.h:48:3: error: 'reverseInPlace' was not declared in this scope, and 
> no declarations were found by argument-dependent lookup at the point of 
> instantiation [-fpermissive]
> alphabet.h:74:20: note: 'template void reverseInPlace(TStr&)' 
> declared here, later in the translation unit
> In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>  from SeqAn-1.1/seqan/index.h:27,
>  from ebwt_build.cpp:5:
> SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct 
> seqan::_PackedConsts seqan::_Dna>, seqan::Packed<> > >':
> SeqAn-1.1/seqan/sequence/string_packed.h:906:131:   required from 'typename 
> seqan::Position > 
> >::Type seqan::position(const seqan::Iter seqan::Packed >&) [with TContainer = const 
> seqan::String, seqan::Packed<> 
> >; THostspec = seqan::Alloc; typename seqan::Position seqan::Iter > >::Type = long unsigned 
> int]'
> SeqAn-1.1/seqan/sequence/string_packed.h:1237:40:   required from 'typename 
> seqan::Difference > >::Type 
> seqan::operator-(const seqan::Iter >&, 
> const seqan::Iter >&) [with TContainer = 
> const seqan::String, 
> seqan::Packed<> >; THostspec = seqan::Alloc; typename 
> seqan::Difference > >::Type 
> = long int]'
> SeqAn-1.1/seqan/sequence/string_base.h:181:51:   required from 'typename 
> seqan::Size >::Type seqan::length(const 
> seqan::String&) [with TValue = seqan::SimpleType char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size seqan::String >::Type = long unsigned int]'
> blockwise_sa.h:354:32:   required from here
> SeqAn-1.1/seqan/sequence/string_packed.h:291:2: warning: comparison between 
> 'enum seqan::BitsPerValue 
> >::' and 'enum seqan::BitsPerValue::' 
> [-Wenum-compare]
> SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct 
> seqan::_PackedConsts seqan::_Dna>, seqan::Packed<> > >':
> SeqAn-1.1/seqan/sequence/string_packed.h:731:94:   required from 'typename 
> seqan::Size > >::Type 
> seqan::reserve(seqan::String >&, _TSize, 
> seqan::Tag) [with TValue = seqan::SimpleType seqan::_Dna>; TSpec = seqan::Alloc; _TSize = long unsigned int; TExpand 
> = seqan::TagExact_; typename seqan::Size seqan::Packed > >::Type = long unsigned int]'
> ebwt.h:3891:2:   required from 'static TStr 
> Ebwt::join(std::vector&, std::vector&, uint32_t, 
> const RefReadInParams&, uint32_t) [with TStr = 
> seqan::String, seqan::Packed<> 
> >; uint32_t = unsigned int]'
> ebwt_build.cpp:463:9:   required from 'v

Re: Help needed [Was: Bug#667325: plink: ftbfs with GCC-4.7]

2012-04-22 Thread Dmitry Nezhevenko
On Sun, Apr 22, 2012 at 09:45:42PM +0200, Andreas Tille wrote:
> Hi,
> 
> I tried to follow the hints to fix this problem but failed.
> Any more skilled C++ programmer than me who might have a clue?

Hi,

It's just incorrect code (sets.cpp):

 703   for (int i=0; i count;
 708   vector acount;
...
 771   vector::iterator i = PP->sample.begin();
 772   while ( i != PP->sample.end() )
 773 {
 774   (*i)->missing = (*i)->flag;
 775   ++i;
 776 }

As you can see, there is nested declaration here. It's wrong. Looks like
this code was working due to some GCC bug. Other compilers forbids this
too. So just change lines 771-776 to use some other variable name.

Regards
 
-- 
WBR, Dmitry


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Re: Help needed to fix g++ 4.7 error [Was: Bug#667120: bowtie: ftbfs with GCC-4.7]

2012-04-22 Thread gregor herrmann
On Sun, 22 Apr 2012 22:15:04 +0200, Andreas Tille wrote:

> similarly to the plink case I can not found an easy solution for this
> problem.

> alphabet.h:48:3: error: 'reverseInPlace' was not declared in this scope, and 
> no declarations were found by argument-dependent lookup at the point of 
> instantiation [-fpermissive]

Moving reverseInPlace before reverseComplementInPlace (which uses the
former) in alphabet.h seems to be enough.

Cheers,
gregor 
 
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 `. `'  Member of VIBE!AT & SPI, fellow of the Free Software Foundation Europe
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Re: Help needed [Was: Bug#667325: plink: ftbfs with GCC-4.7]

2012-04-22 Thread Rodolfo García Peñas
On Sun, 22 Apr 2012, Andreas Tille escribió:

> Hi,
> 
> I tried to follow the hints to fix this problem but failed.
> Any more skilled C++ programmer than me who might have a clue?
> 
> Kind regards
> 
>  Andreas.
> 
[snip]
> - Forwarded message from Matthias Klose  -
> sets.cpp:703:31: warning: comparison between signed and unsigned integer 
> expressions [-Wsign-compare]
> sets.cpp:713:43: warning: comparison between signed and unsigned integer 
> expressions [-Wsign-compare]
> sets.cpp:771:37: error: redeclaration of 'std::vector::iterator 
> i'
> sets.cpp:703:12: error: 'int i' previously declared here
> sets.cpp: In member function 'vector_t Set::fitLDSetTest(vector_t&, bool)':
> sets.cpp:905:31: warning: comparison between signed and unsigned integer 
> expressions [-Wsign-compare]
> sets.cpp:975:34: warning: comparison between signed and unsigned integer 
> expressions [-Wsign-compare]
> sets.cpp: In member function 'vector_t Set::fitStepwiseModel()':
> sets.cpp:1042:31: warning: comparison between signed and unsigned integer 
> expressions [-Wsign-compare]
> make[1]: *** [sets.o] Error 1
> make[1]: Leaving directory `/??PKGBUILDDIR??'
> make: *** [build-stamp] Error 2
> dpkg-buildpackage: error: debian/rules build gave error exit status 2
> 

Hi Andreas,

the problem seems to be that the variable "i" was defined at "sets.cpp:703" 
(see the for(int i...)) and redefined as 'std::vector::iterator i' 
at sets.cpp:771.

Probably renaming i to other name solves the problem. For example:

  vector::iterator i2 = PP->sample.begin();
  while ( i2 != PP->sample.end() )
{
  (*i2)->missing = (*i2)->flag;
  ++i2;
}

Saludos,
kix
 
PS. The code is so dirty, with unused variables,...
> 
> 
> ___
> Debian-med-packaging mailing list
> debian-med-packag...@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
> 
> 
> - End forwarded message -
> 
> -- 
> http://fam-tille.de
> 
> 
> -- 
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> 

-- 
||// //\\// Rodolfo "kix" Garcia
||\\// //\\ http://www.kix.es/


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Re: Help needed [Was: Bug#667325: plink: ftbfs with GCC-4.7]

2012-04-22 Thread Fernando Lemos
Hi,

On Sun, Apr 22, 2012 at 5:37 PM, Dmitry Nezhevenko  wrote:
> As you can see, there is nested declaration here. It's wrong. Looks like
> this code was working due to some GCC bug. Other compilers forbids this
> too.

To expand/clarify, this is not a "nested declaration", but rather a
redefinition of a variable that was declared in the same scope.
Redefining variables in different scopes is fine. So if i were
declared outside the scope of the for loop, this would be okay (this
is called shadowing).

Apparently, g++ up to 4.6 considered the scope of a variable declared
in a for loop to be the "outer" scope, instead of the "inner"
scope[1][2]. This explains the problem.

[1]: http://gcc.gnu.org/gcc-4.7/porting_to.html
[2]: http://gcc.gnu.org/bugzilla/show_bug.cgi?id=2288

Regards,


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Bug#659083: RFS: xmoto -- 2D motocross platform game

2012-04-22 Thread Stephen Kitt
tag 659083 - moreinfo
thanks

Hi Ansgar,

It's been ages, but I've finally finished getting everything ready.

On Sun, 26 Feb 2012 15:52:56 +0100, Ansgar Burchardt 
wrote:
> Stephen Kitt  writes:
> >   dget -x
> > http://mentors.debian.net/debian/pool/main/x/xmoto/xmoto_0.5.9-1.dsc
> 
> You do not include the full license text for src/glext.h in the
> copyright information.

I should have noticed that... It was actually not DFSG-free, but it's easy
enough to patch out so I've repacked the upstream tarball without it (and
with the small, necessary patch; I added a README.dfsg file to explain
everything). I filed a bug upstream too.

> Have the patches been forwarded upstream?

They have now, see the updated patch headers for details.

> You use debhelper compat level 9, so why don't you build-depend on
> debhelper (>= 9)?

When I initially switched to compat level 9, debhelper 9 wasn't available
yet. I changed the build-dependency to (>= 9).

> Please update at least config.{guess,sub}, see [1] for details, or just
> use dh-autoreconf (my personal preference).

I like dh-autoreconf too, that's what I went for.

> The source for bin/xmoto.bin seems to be missing, compare with
> upstream's SVN repository[2].  I have filed a bug[3] as it is also
> the case for the version currently inthe archive.  Please ask upstream
> to include the source and ideally built xmoto.bin instead of including
> it, see also [4] for more details.

Indeed; I took the opportunity of repacking the upstream tarball to add the
missing files and remove xmoto.bin. (The resulting build still produces an
identical xmoto.bin.) I also forwarded your bug upstream.

All this (and more) is available in the subversion repository and at
http://mentors.debian.net/debian/pool/main/x/xmoto/xmoto_0.5.9+dfsg-1.dsc

The changelog is as follows:

xmoto (0.5.9+dfsg-1) unstable; urgency=low

  * New upstream release (closes: #644234):
+ builds with libpng 1.5 (closes: #649797);
+ uses libxml2;
+ uses DejaVuSansMono (add link and make ttf-dejavu-core a dependency
  of xmoto-data).
  * Repacked to avoid licensing problems:
+ remove src/glext.h, licensed under SGI License B version 1.1;
+ add the missing contents in bin (closes: #661340).
(I'm hoping that both issues will be fixed upstream, so I haven't
added a get-orig-source target to debian/rules. README.dfsg in the
repacked source explains the changes.)
  * Update debian/watch accordingly.
  * Update patches:
+ fix_segfault.patch: refresh, add DEP-3 header, forward upstream;
+ desktop.patch: re-apply, add German translation (closes: #641822),
  forward upstream;
+ spelling.patch: refresh, forward upstream;
+ manpage.patch: forward upstream;
+ gcc44-ftbfs.patch: no longer used, delete.
  * Switch to dh 9 with simple rules.
  * Use source format "3.0 (quilt)".
  * Add ${misc:Depends} where appropriate.
  * Patch the manpage to fix hyphens and a few spelling mistakes.
  * Add myself to uploaders.
  * Update debian/copyright.
  * Standards-Version 3.9.3 (no further change required).
  * Fix spelling mistakes spotted by Lintian.
  * Use dh-autoreconf to update config.{guess,sub} (thanks to Ansgar
Burchardt for the hint).
  * wrap-and-sort control files.
  * Build-depend on libpng-dev only, dropping the libpng12-dev alternative
(closes: #662565).
  * Fix "ftbfs with GCC-4.7" by including unistd.h where appropriate
(closes: #667422; thanks to Cyril Brulebois for his patch for another
gcc-4.7-related issue, which was already included upstream).
  * Fix the Vcs-Browser URL.

 -- Stephen Kitt   Mon, 23 Apr 2012 00:19:42 +0200

Regards,

Stephen


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Processed: Re: Bug#659083: RFS: xmoto -- 2D motocross platform game

2012-04-22 Thread Debian Bug Tracking System
Processing commands for cont...@bugs.debian.org:

> tag 659083 - moreinfo
Bug #659083 [sponsorship-requests] RFS: xmoto -- 2D motocross platform game
Removed tag(s) moreinfo.
> thanks
Stopping processing here.

Please contact me if you need assistance.
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Bug#670064: RFS: dylandotnet/11.2.9.2-1 [ITP] -- dylandotnet compiler

2012-04-22 Thread Ansgar Burchardt
tag 670064 + moreinfo
block 626078 with 670064

Dylan Borg  writes:
> dget -x 
> http://mentors.debian.net/debian/pool/main/d/dylandotnet/dylandotnet_11.2.9.2-1.dsc

Half of the comments from [1] still seem to apply to the current
package.  In addition there are many file in the upstream tarball that
should not be there such as backup copies or log files.

Also the following is not a useful changelog entry:

>   dylandotnet (11.2.9.2-1) experimental; urgency=low
>   
> * (Closes:626078)
>   
>-- Dylan Borg   Sun, 21 Apr 2012 18:57:04 +0100

Please take a look at section 6.3 of the developer reference[2].  Please
also read the part about the package description (6.2.1-3).

Is the language the compiler is written for used anywhere?

Regards,
Ansgar

[1] 
[2] 



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Processed (with 5 errors): Re: Bug#670064: RFS: dylandotnet/11.2.9.2-1 [ITP] -- dylandotnet compiler

2012-04-22 Thread Debian Bug Tracking System
Processing commands for cont...@bugs.debian.org:

> tag 670064 + moreinfo
Bug #670064 [sponsorship-requests] RFS: dylandotnet/11.2.9.2-1 [ITP] -- 
dylandotnet compiler
Added tag(s) moreinfo.
> block 626078 with 670064
Bug #626078 [wnpp] ITP: dylandotnet -- This is the dylan.NET compiler.
626078 was not blocked by any bugs.
626078 was not blocking any bugs.
Added blocking bug(s) of 626078: 670064
> Dylan Borg  writes:
Unknown command or malformed arguments to command.

> > dget -x 
> > http://mentors.debian.net/debian/pool/main/d/dylandotnet/dylandotnet_11.2.9.2-1.dsc
Unknown command or malformed arguments to command.

> Half of the comments from [1] still seem to apply to the current
Unknown command or malformed arguments to command.

> package.  In addition there are many file in the upstream tarball that
Unknown command or malformed arguments to command.

> should not be there such as backup copies or log files.
Unknown command or malformed arguments to command.

Too many unknown commands, stopping here.

Please contact me if you need assistance.
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Re: Bug#669401: RFS: roxterm/2.6.2-1 (was 2.6.1-1)

2012-04-22 Thread Kan-Ru Chen
Uploaded.

Thanks for your contribution!

  Kanru

Tony Houghton  writes:

> retitle 669401 RFS: roxterm/2.6.2-1
> thanks
>
> The Ubuntu PPA builder for lucid uncovered a backwards compatibility bug
> so I've updated upstream and replaced the package so that uscan won't
> complain about its not being the latest upstream.
>
> dget -x 
> http://mentors.debian.net/debian/pool/main/r/roxterm/roxterm_2.6.2-1.dsc
>
> On Thu, 19 Apr 2012 16:03:13 +0100
> Tony Houghton  wrote:
>
>> I am looking for a sponsor for my package "roxterm"
>> 
>> * Package name: roxterm
>>   Version : 2.6.1-1
>>   Upstream Author : Tony Houghton 
>>   URL : http://roxterm.sourceforge.net
>>   License : GPL2+
>>   Section : x11
>> 
>> It builds those binary packages:
>> 
>> * roxterm - Multi-tabbed GTK+/VTE terminal emulator - virtual package for 
>> GTK3
>> * roxterm-common - Multi-tabbed GTK+/VTE terminal emulator - common files
>> * roxterm-gtk2 - Multi-tabbed GTK+/VTE terminal emulator - GTK2 version
>> * roxterm-gtk3 - Multi-tabbed GTK+/VTE terminal emulator - GTK3 version
>> 
>> To access further information about this package, please visit the
>> following URL:
>> 
>> http://mentors.debian.net/package/roxterm
>> 
>> 
>> Alternatively, one can download the package with dget using this
>> command:
>> 
>>   dget -x
>>   http://mentors.debian.net/debian/pool/main/r/roxterm/roxterm_2.6.1-1.dsc
>> 
>> More information about roxterm can be obtained from
>> http://roxterm.sourceforge.net
>> 
>> Changes since the last upload:
>> 
>>   * Ensure vte widgets realized before reading xid (Closes: #663736).
>>   * Explicitly close pty when deleting a terminal.
>>   * Warnings apply to closing windows via menu (Closes: #664887).
>>   * Debian packaging now maintained in master branch again.
>>   * Changed close warning dialog buttons to Yes/No.
>>   * Honour login option when restoring a session (Closes: #663739).
>>   * Reread GdkWindow when re-mapping windows when compositing changes.
>>   * debian/watch: Corrected pcre syntax for uncaptured bz2/gz suffix. 
>

-- 
Kanru


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Bug#669401: marked as done (RFS: roxterm/2.6.2-1)

2012-04-22 Thread Debian Bug Tracking System
Your message dated Mon, 23 Apr 2012 08:05:23 +0800
with message-id <87obqjtirg@isil.kanru.info>
and subject line Re: Bug#669401: RFS: roxterm/2.6.2-1 (was 2.6.1-1)
has caused the Debian Bug report #669401,
regarding RFS: roxterm/2.6.2-1
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
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immediately.)


-- 
669401: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=669401
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: sponsorship-requests
Severity: normal [important for RC bugs, wishlist for new packages]

Dear mentors,

I am looking for a sponsor for my package "roxterm"

* Package name: roxterm
  Version : 2.6.1-1
  Upstream Author : Tony Houghton 
  URL : http://roxterm.sourceforge.net
  License : GPL2+
  Section : x11

It builds those binary packages:

* roxterm - Multi-tabbed GTK+/VTE terminal emulator - virtual package for GTK3
* roxterm-common - Multi-tabbed GTK+/VTE terminal emulator - common files
* roxterm-gtk2 - Multi-tabbed GTK+/VTE terminal emulator - GTK2 version
* roxterm-gtk3 - Multi-tabbed GTK+/VTE terminal emulator - GTK3 version

To access further information about this package, please visit the
following URL:

http://mentors.debian.net/package/roxterm


Alternatively, one can download the package with dget using this
command:

  dget -x
  http://mentors.debian.net/debian/pool/main/r/roxterm/roxterm_2.6.1-1.dsc

More information about roxterm can be obtained from
http://roxterm.sourceforge.net

Changes since the last upload:

  * Ensure vte widgets realized before reading xid (Closes: #663736).
  * Explicitly close pty when deleting a terminal.
  * Warnings apply to closing windows via menu (Closes: #664887).
  * Debian packaging now maintained in master branch again.
  * Changed close warning dialog buttons to Yes/No.
  * Honour login option when restoring a session (Closes: #663739).
  * Reread GdkWindow when re-mapping windows when compositing changes.
  * debian/watch: Corrected pcre syntax for uncaptured bz2/gz suffix. 

Regards,
 Tony Houghton


--- End Message ---
--- Begin Message ---
Uploaded.

Thanks for your contribution!

  Kanru

Tony Houghton  writes:

> retitle 669401 RFS: roxterm/2.6.2-1
> thanks
>
> The Ubuntu PPA builder for lucid uncovered a backwards compatibility bug
> so I've updated upstream and replaced the package so that uscan won't
> complain about its not being the latest upstream.
>
> dget -x 
> http://mentors.debian.net/debian/pool/main/r/roxterm/roxterm_2.6.2-1.dsc
>
> On Thu, 19 Apr 2012 16:03:13 +0100
> Tony Houghton  wrote:
>
>> I am looking for a sponsor for my package "roxterm"
>> 
>> * Package name: roxterm
>>   Version : 2.6.1-1
>>   Upstream Author : Tony Houghton 
>>   URL : http://roxterm.sourceforge.net
>>   License : GPL2+
>>   Section : x11
>> 
>> It builds those binary packages:
>> 
>> * roxterm - Multi-tabbed GTK+/VTE terminal emulator - virtual package for 
>> GTK3
>> * roxterm-common - Multi-tabbed GTK+/VTE terminal emulator - common files
>> * roxterm-gtk2 - Multi-tabbed GTK+/VTE terminal emulator - GTK2 version
>> * roxterm-gtk3 - Multi-tabbed GTK+/VTE terminal emulator - GTK3 version
>> 
>> To access further information about this package, please visit the
>> following URL:
>> 
>> http://mentors.debian.net/package/roxterm
>> 
>> 
>> Alternatively, one can download the package with dget using this
>> command:
>> 
>>   dget -x
>>   http://mentors.debian.net/debian/pool/main/r/roxterm/roxterm_2.6.1-1.dsc
>> 
>> More information about roxterm can be obtained from
>> http://roxterm.sourceforge.net
>> 
>> Changes since the last upload:
>> 
>>   * Ensure vte widgets realized before reading xid (Closes: #663736).
>>   * Explicitly close pty when deleting a terminal.
>>   * Warnings apply to closing windows via menu (Closes: #664887).
>>   * Debian packaging now maintained in master branch again.
>>   * Changed close warning dialog buttons to Yes/No.
>>   * Honour login option when restoring a session (Closes: #663739).
>>   * Reread GdkWindow when re-mapping windows when compositing changes.
>>   * debian/watch: Corrected pcre syntax for uncaptured bz2/gz suffix. 
>

-- 
Kanru

--- End Message ---


Bug#667437: marked as done (RFS: 4digits/1.1-1 QA)

2012-04-22 Thread Debian Bug Tracking System
Your message dated Mon, 23 Apr 2012 09:04:19 +0800
with message-id 

and subject line Close
has caused the Debian Bug report #667437,
regarding RFS: 4digits/1.1-1 QA
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
667437: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=667437
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: sponsorship-requests
Severity: normal

Dear mentors,

I am looking for a sponsor for my package "4digits"

* Package name : 4digits
Version : 1.1-1
Upstream Author : Yongzhi Pan 
* URL : http://sourceforge.net/projects/fourdigits


* License : GPL v2
Section : games

It builds those binary packages:

4digits - guess-the-number game, aka Bulls and Cows

To access further information about this package, please visit the
following URL:

http://mentors.debian.net/package/4digits




Alternatively, one can download the package with dget using this command:

dget -x
http://mentors.debian.net/debian/pool/main/4/4digits/4digits_1.1-1.dsc



Changes since the last upload:

* New upstream version.
* Added debian patch to fix resoure directories.

Regards,
Yongzhi Pan
--- End Message ---
--- Begin Message ---
The package is now uploaded to the master FTP. Bug resolved.

-- 
Regards,

Yongzhi Pan
--- End Message ---


maximal or minimal deletion when creating dfsg tarball?

2012-04-22 Thread Paul Elliott
My package source tarball contains some "convenience copies of code". I have 
modified the package to use to the external package instead, so this code is 
now unneeded and unused.

Unfortunately, my upsteam's upstream, (ie. the source my upstream copied 
from), also included some unsourced binaries (documentation in the form of 
.pdf), with this code.

Except for the unsourced binaries, this code is properly licenced.

I must remove these, creating a dfsg tarball.

It has been suggested by a respected reviewer that while I am removing the 
unsourced binaries, I remove ALL of the "convenience copies of code". That way 
the unused code would not confuse anyone.

I thought, that when creating a dfsg tarball, one should remove only the files 
with licensing problems.

What is the proper procedure? Remove only the unsourced binaries, or all of 
the unused code?

-- 
Paul Elliott   1(512)837-1096
pelli...@blackpatchpanel.com   PMB 181, 11900 Metric Blvd Suite J
http://www.free.blackpatchpanel.com/pme/   Austin TX 78758-3117


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Bug#670064: (no subject)

2012-04-22 Thread Dylan Borg
the logs may be removed.
The binaries in the 2.0 and 4.0 directories may not since they are used in the 
build to remake them.
As for the log,the latest version is an adaptation of a previous version 
released in a ppa. The full log can be found in the package.

Regards,
  Dylan Borg
  borgdy...@hotmail.com
  borgdyl...@gmail.com
  dbor0...@um.edu.mt
  +0035699214902