gmp_6.1.2+dfsg-1_i386.changes ACCEPTED into unstable

2016-12-20 Thread Debian FTP Masters 


Accepted:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 20 Dec 2016 23:39:47 -0600
Source: gmp
Binary: libgmp10 libgmpxx4ldbl libgmp-dev libgmp10-doc libgmp3-dev
Architecture: source i386 all
Version: 2:6.1.2+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Team 

Changed-By: Steve M. Robbins 
Description:
 libgmp-dev - Multiprecision arithmetic library developers tools
 libgmp10   - Multiprecision arithmetic library
 libgmp10-doc - Multiprecision arithmetic library example code
 libgmp3-dev - Multiprecision arithmetic library developers tools
 libgmpxx4ldbl - Multiprecision arithmetic library (C++ bindings)
Changes:
 gmp (2:6.1.2+dfsg-1) unstable; urgency=medium
 .
   * New upstream.
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gmp_6.1.2+dfsg-1_i386.buildinfo
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libgmp-dev_6.1.2+dfsg-1_i386.deb
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libgmp10-dbgsym_6.1.2+dfsg-1_i386.deb
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libgmp10_6.1.2+dfsg-1_i386.deb
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libgmpxx4ldbl-dbgsym_6.1.2+dfsg-1_i386.deb
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libgmpxx4ldbl_6.1.2+dfsg-1_i386.deb

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Processing of gmp_6.1.2+dfsg-1_i386.changes

2016-12-20 Thread Debian FTP Masters 
gmp_6.1.2+dfsg-1_i386.changes uploaded successfully to localhost
along with the files:
  gmp_6.1.2+dfsg-1.dsc
  gmp_6.1.2+dfsg.orig.tar.xz
  gmp_6.1.2+dfsg-1.debian.tar.xz
  gmp_6.1.2+dfsg-1_i386.buildinfo
  libgmp-dev_6.1.2+dfsg-1_i386.deb
  libgmp10-dbgsym_6.1.2+dfsg-1_i386.deb
  libgmp10-doc_6.1.2+dfsg-1_all.deb
  libgmp10_6.1.2+dfsg-1_i386.deb
  libgmp3-dev_6.1.2+dfsg-1_i386.deb
  libgmpxx4ldbl-dbgsym_6.1.2+dfsg-1_i386.deb
  libgmpxx4ldbl_6.1.2+dfsg-1_i386.deb

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Bug#848899: marked as done (flint: Conflicting definition of count_leading_zeros in givaro affects flint)

2016-12-20 Thread Debian Bug Tracking System 
Your message dated Wed, 21 Dec 2016 01:04:34 +
with message-id 
and subject line Bug#848899: fixed in flint 2.5.2-14
has caused the Debian Bug report #848899,
regarding flint: Conflicting definition of count_leading_zeros in givaro 
affects flint
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.)


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Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: flint
Version: 2.5.2-13


Hi,

On arm64 and ppc64el sagemath fails to build while trying to compile
/«PKGBUILDDIR»/sage/src/build/cythonized/sage/matrix/matrix_mpolynomial_dense.cpp

This is the relevant error:

[sagelib-7.4] In file included from /usr/include/recint/recdefine.h:145:0,
[sagelib-7.4]  from /usr/include/recint/ruruint.h:43,
[sagelib-7.4]  from /usr/include/recint/rumanip.h:41,
[sagelib-7.4]  from /usr/include/recint/ruconvert.h:43,
[sagelib-7.4]  from /usr/include/gmp++/gmp++_int.h:26,
[sagelib-7.4]  from /usr/include/gmp++/gmp++.h:56,
[sagelib-7.4]  from /usr/include/givaro/givinteger.h:19,
[sagelib-7.4]  from /usr/include/givaro/modular-int8.h:29,
[sagelib-7.4]  from /usr/include/givaro/modular.h:21,
[sagelib-7.4]  from
/«PKGBUILDDIR»/sage/src/build/cythonized/sage/matrix/matrix_modn_dense_double.cpp:532:
[sagelib-7.4] /usr/include/flint/flint.h: In function 'unsigned int
FLINT_BIT_COUNT(mp_limb_t)':
[sagelib-7.4] /usr/include/flint/flint.h:257:11: error: 'UWtype' was not
declared in this scope
[sagelib-7.4] if (x) count_leading_zeros(zeros, x);
[sagelib-7.4]^
[sagelib-7.4] /usr/include/flint/flint.h:257:11: note: suggested
alternative:
[sagelib-7.4] In file included from /usr/include/recint/ruruint.h:43:0,
[sagelib-7.4]  from /usr/include/recint/rumanip.h:41,
[sagelib-7.4]  from /usr/include/recint/ruconvert.h:43,
[sagelib-7.4]  from /usr/include/gmp++/gmp++_int.h:26,
[sagelib-7.4]  from /usr/include/gmp++/gmp++.h:56,
[sagelib-7.4]  from /usr/include/givaro/givinteger.h:19,
[sagelib-7.4]  from /usr/include/givaro/modular-int8.h:29,
[sagelib-7.4]  from /usr/include/givaro/modular.h:21,
[sagelib-7.4]  from
/«PKGBUILDDIR»/sage/src/build/cythonized/sage/matrix/matrix_modn_dense_double.cpp:532:
[sagelib-7.4] /usr/include/recint/recdefine.h:127:22: note:  
'RecInt::UWtype'
[sagelib-7.4]  typedef uint64_t UWtype;
[sagelib-7.4]   ^~


count_leading_zeros is defined in flints longlong.h. There are several
architecture specific implementations and then in the end this:

#ifndef count_leading_zeros
#define count_leading_zeros(count, x)
...
and similar for count_trailing_zeros.

In our case it seems that count_leading_zeros was already defined in
givaros reclonglong.h so if there is not architecture specific
implementation in longlong.h, the fallback does not work. For the logic
to work we can put in the beginning of longlong.h:

#undef count_leading_zeros
#undef count_trailing_zeros

I didn't test it yet.

Best,
Tobias
--- End Message ---
--- Begin Message ---
Source: flint
Source-Version: 2.5.2-14

We believe that the bug you reported is fixed in the latest version of
flint, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 848...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Tobias Hansen  (supplier of updated flint package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 21 Dec 2016 00:34:03 +
Source: flint
Binary: libflint-2.5.2 libflint-dev libflint-doc
Architecture: source
Version: 2.5.2-14
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Tobias Hansen 
Description:
 libflint-2.5.2 - C library for number theory, shared library
 libflint-dev - C library for number theory, development

flint_2.5.2-14_source.changes ACCEPTED into unstable

2016-12-20 Thread Debian FTP Masters 


Accepted:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 21 Dec 2016 00:34:03 +
Source: flint
Binary: libflint-2.5.2 libflint-dev libflint-doc
Architecture: source
Version: 2.5.2-14
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Tobias Hansen 
Description:
 libflint-2.5.2 - C library for number theory, shared library
 libflint-dev - C library for number theory, development files
 libflint-doc - Documentation for the FLINT library
Closes: 848899
Changes:
 flint (2.5.2-14) unstable; urgency=medium
 .
   * Team upload.
   * New patch undef_count_leading_zeros.patch:
 Avoid problems when using flint together with givaro. (Closes: #848899)
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Processing of flint_2.5.2-14_source.changes

2016-12-20 Thread Debian FTP Masters 
flint_2.5.2-14_source.changes uploaded successfully to localhost
along with the files:
  flint_2.5.2-14.dsc
  flint_2.5.2-14.debian.tar.xz

Greetings,

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Processed: Re: [src:dx] FTBFS dx

2016-12-20 Thread Debian Bug Tracking System 
Processing control commands:

> tags -1 moreinfo
Bug #848894 [src:dx] [src:dx] FTBFS dx
Added tag(s) moreinfo.

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Processed: eigen3: autopkgtests fail on ppc64el

2016-12-20 Thread Debian Bug Tracking System 
Processing commands for cont...@bugs.debian.org:

> tags 836844 pending
Bug #836844 [src:eigen3] eigen3: autopkgtests fail on ppc64el
Added tag(s) pending.
> thanks
Stopping processing here.

Please contact me if you need assistance.
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Re: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

2016-12-20 Thread Anton Gladky 
2016-12-20 15:01 GMT+01:00 Sandro Tosi :
>> it seems the recent upgrade of numpy has broken some tests in other
>> packages like for instance this one in python-skbio.  I wonder whether
>> you are either able to suggest patches to get the tests working with the
>> new interface of numpy again or whether it might be sensible to revert
>> the upgrade of python-numpy to the previous version considering that we
>> are quite close to the freeze.
>
> There is still a month to the freeze for the existing package, so
> let's not panic already. I'd suggest contacting the upstream of the
> projects with failing test and ask for support

I do support Andreas' statement and ask to revert numpy upload if patches
for the dependent packages are not available. We are too close to the freeze
to fix many new bugs and Christmas time will unlikely motivate upstream people
to fix new "numpy API". Semi-transitions should be avoided already.

Thanks

Anton

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Bug#848913: libeigen3-doc is no longer built

2016-12-20 Thread Yd 

Package: libeigen3-doc
Version: 3.3.0-1
Severity: normal

The package libeigen3-doc doesn't seem to be built any longer, but it's still
suggested by libeigen3-dev.

It would be nice if the package would be built again.

-- System Information:
Debian Release: stretch/sid
 APT prefers unstable
 APT policy: (900, 'unstable'), (800, 'experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 4.9.0-rc8-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages libeigen3-doc depends on:
ii  fonts-freefont-ttf  20120503-6
ii  libjs-jquery3.1.1-2

libeigen3-doc recommends no packages.

Versions of packages libeigen3-doc suggests:
ii  libeigen3-dev  3.3.0-1

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Processed: Correct version with the epoch

2016-12-20 Thread Debian Bug Tracking System 
Processing commands for cont...@bugs.debian.org:

> notfound 848894 4.4.4-9
Bug #848894 [src:dx] [src:dx] FTBFS dx
The source 'dx' and version '4.4.4-9' do not appear to match any binary packages
No longer marked as found in versions dx/4.4.4-9.
> found 848894 1:4.4.4-9
Bug #848894 [src:dx] [src:dx] FTBFS dx
Marked as found in versions dx/1:4.4.4-9.
> thanks
Stopping processing here.

Please contact me if you need assistance.
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Bug#848747: marked as done (syrthes: FTBFS: H5public.h:61:20: fatal error: mpi.h: No such file or directory)

2016-12-20 Thread Debian Bug Tracking System 
Your message dated Tue, 20 Dec 2016 18:03:33 +
with message-id 
and subject line Bug#848747: fixed in syrthes 4.3.0-dfsg1-2
has caused the Debian Bug report #848747,
regarding syrthes: FTBFS: H5public.h:61:20: fatal error: mpi.h: No such file or 
directory
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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--- Begin Message ---
Source: syrthes
Version: 4.3.0-dfsg1-1
Severity: serious
Tags: stretch sid
User: debian...@lists.debian.org
Usertags: qa-ftbfs-20161219 qa-ftbfs
Justification: FTBFS on amd64

Hi,

During a rebuild of all packages in sid, your package failed to build on
amd64.

Relevant part (hopefully):
> gcc -c  -D _FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<>=. 
> -fstack-protector-strong -Wformat -Werror=format-security -D_SYRTHES_MPI_ 
> -DMED -I /usr/lib/openmpi/include -I/usr/include 
> -I/usr/lib/x86_64-linux-gnu/hdf5/openmpi/include convert2syrthes4.c -o 
> ../../../../build//convert2syrthes4.o
> lecture_sim.c: In function 'lecture_tableau_sim_entier':
> lecture_sim.c:186:22: warning: format '%d' expects argument of type 'int', 
> but argument 3 has type 'long int' [-Wformat=]
>   printf("_tab[%d] = %d\n",j,_tab[j]);
>   ^
> lecture_sim.c:188:11: warning: format '%d' expects argument of type 'int', 
> but argument 2 has type 'long int' [-Wformat=]
>   printf("%d != %d\n",_tab[0],l_seg);
>^
> lecture_sim.c:195:24: warning: format '%d' expects argument of type 'int', 
> but argument 3 has type 'long int' [-Wformat=]
>   printf("_tab[%d+1] = %d\n",j,_tab[j+1]);
> ^
> lecture_sim.c:202:22: warning: format '%d' expects argument of type 'int', 
> but argument 3 has type 'long int' [-Wformat=]
>   printf("_tab[%d] = %d\n",i,_tab[0]);
>   ^
> lecture_sim.c: In function 'lire_sim':
> lecture_sim.c:391:32: warning: format '%d' expects argument of type 'int', 
> but argument 2 has type 'long int' [-Wformat=]
>  printf("m[   30] NIVEAU = %d\n",  m[29]);
> ^
> lecture_sim.c:392:32: warning: format '%d' expects argument of type 'int', 
> but argument 2 has type 'long int' [-Wformat=]
>  printf("m[   31] ETAT   = %d\n",  m[30]);
> ^
> lecture_sim.c:393:32: warning: format '%d' expects argument of type 'int', 
> but argument 2 has type 'long int' [-Wformat=]
>  printf("m[   32] NTACM  = %d\n",  m[31]);
> ^
> In file included from 
> /usr/lib/x86_64-linux-gnu/hdf5/openmpi/include/hdf5.h:24:0,
>  from /usr/include/med.h:22,
>  from lecture_med.c:44:
> /usr/include/hdf5/openmpi/H5public.h:61:20: fatal error: mpi.h: No such file 
> or directory
>  #   include 
> ^
> compilation terminated.
> lecture_sim.c:699:2: warning: implicit declaration of function 'extrbord2' 
> [-Wimplicit-function-declaration]
>   extrbord2(*maillnodes,maillnodebord,nrefac);
>   ^
> lecture_sim.c:701:2: warning: implicit declaration of function 'extrbord3' 
> [-Wimplicit-function-declaration]
>   extrbord3(*maillnodes,maillnodebord,nrefac);
>   ^
> convert2syrthes4.c: In function 'main':
> convert2syrthes4.c:191:9: warning: implicit declaration of function 
> 'ouvrir_syr' [-Wimplicit-function-declaration]
>  if (ouvrir_syr(,nom_syr) != 0) return 1;
>  ^~
> convert2syrthes4.c:197:16: warning: implicit declaration of function 
> 'conversion_neu' [-Wimplicit-function-declaration]
>case 1 : if (conversion_neu(,iargv[m+1]) != 0) return 1; break;
> ^~
> convert2syrthes4.c:198:16: warning: implicit declaration of function 
> 'conversion_msh' [-Wimplicit-function-declaration]
>case 2 : if (conversion_msh(,iargv[m+1]) != 0) return 1; break;
> ^~
> convert2syrthes4.c:200:16: warning: implicit declaration of function 
> 'conversion_med' [-Wimplicit-function-declaration]
>case 3 : if (conversion_med(,iargv[m+1], nom_syr) != 0) return 1; 
> break;
> ^~
> convert2syrthes4.c:202:16: warning: implicit declaration of function 
> 'conversion_sim' [-Wimplicit-function-declaration]
>case 4 : if 
> (conversion_sim(,,,iargv[m+1], nom_syr) != 
> 0) return 1; break;
> ^~
> convert2syrthes4.c:203:16: warning: implicit declaration of function 
> 'conversion_ide' [-Wimplicit-function-declaration]
>case 5 : if

syrthes_4.3.0-dfsg1-2_source.changes ACCEPTED into unstable

2016-12-20 Thread Debian FTP Masters 


Accepted:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 20 Dec 2016 18:29:18 +0100
Source: syrthes
Binary: syrthes syrthes-tools syrthes-gui syrthes-tests
Architecture: source
Version: 4.3.0-dfsg1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Gilles Filippini 
Description:
 syrthes- Transient thermal simulations in complex solid geometries
 syrthes-gui - Transient thermal simulations in complex solid geometries - GUI
 syrthes-tests - Test cases for SYRTHES
 syrthes-tools - Transient thermal simulations in complex solid geometries - 
tools
Closes: 848747
Changes:
 syrthes (4.3.0-dfsg1-2) unstable; urgency=medium
 .
   * Update patch setup.patch after openmpi went mutiarch (closes:
 #848747)
Checksums-Sha1:
 5bbabeb31a1b9456ad87c29fd8a3da6ade656e21 2014 syrthes_4.3.0-dfsg1-2.dsc
 27e741246b9cd97ddefb204f36579d5a3e7916b0 12824 
syrthes_4.3.0-dfsg1-2.debian.tar.xz
Checksums-Sha256:
 e0e4aba2b25ac0efbbad3c5fc8e6b18a67b6f7cdcfb0183e07e7aefe5402626e 2014 
syrthes_4.3.0-dfsg1-2.dsc
 e087bb8e2a1ff5fefe3bd8a29ecc2737718a4a7c82f221845bcbb5495e513de0 12824 
syrthes_4.3.0-dfsg1-2.debian.tar.xz
Files:
 90c9af04a44f0644d18f4d0ee59905a1 2014 science extra syrthes_4.3.0-dfsg1-2.dsc
 5aa0031d5362410ac4d9dad8e27abed7 12824 science extra 
syrthes_4.3.0-dfsg1-2.debian.tar.xz

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Thank you for your contribution to Debian.

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Processing of syrthes_4.3.0-dfsg1-2_source.changes

2016-12-20 Thread Debian FTP Masters 
syrthes_4.3.0-dfsg1-2_source.changes uploaded successfully to localhost
along with the files:
  syrthes_4.3.0-dfsg1-2.dsc
  syrthes_4.3.0-dfsg1-2.debian.tar.xz

Greetings,

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Bug#848899: Report is unclear

2016-12-20 Thread Julien Puydt 

Hi,

I don't understand why the bug reports ends with a discussion of the 
count_trailing_zeros and count_leading_zeros macros, since the error 
message quoted seems to be about the UWtype typedef.


Notice that I won't have time to have a look before next week (at 
least), so if you find a worthy solution, don't hesitate to team-upload 
a new version!


Snark on #debian-science

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apertium-hbs 0.5.0~r68212-2 MIGRATED to testing

2016-12-20 Thread Debian testing watch 
FYI: The status of the apertium-hbs source package
in Debian's testing distribution has changed.

  Previous version: 0.5.0~r68212-1
  Current version:  0.5.0~r68212-2

-- 
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gmsh 2.15.0+dfsg1-1 MIGRATED to testing

2016-12-20 Thread Debian testing watch 
FYI: The status of the gmsh source package
in Debian's testing distribution has changed.

  Previous version: 2.14.1+dfsg1-1
  Current version:  2.15.0+dfsg1-1

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Bug#848899: flint: Conflicting definition of count_leading_zeros in givaro affects flint

2016-12-20 Thread Tobias Hansen 
Source: flint
Version: 2.5.2-13


Hi,

On arm64 and ppc64el sagemath fails to build while trying to compile
/«PKGBUILDDIR»/sage/src/build/cythonized/sage/matrix/matrix_mpolynomial_dense.cpp

This is the relevant error:

[sagelib-7.4] In file included from /usr/include/recint/recdefine.h:145:0,
[sagelib-7.4]  from /usr/include/recint/ruruint.h:43,
[sagelib-7.4]  from /usr/include/recint/rumanip.h:41,
[sagelib-7.4]  from /usr/include/recint/ruconvert.h:43,
[sagelib-7.4]  from /usr/include/gmp++/gmp++_int.h:26,
[sagelib-7.4]  from /usr/include/gmp++/gmp++.h:56,
[sagelib-7.4]  from /usr/include/givaro/givinteger.h:19,
[sagelib-7.4]  from /usr/include/givaro/modular-int8.h:29,
[sagelib-7.4]  from /usr/include/givaro/modular.h:21,
[sagelib-7.4]  from
/«PKGBUILDDIR»/sage/src/build/cythonized/sage/matrix/matrix_modn_dense_double.cpp:532:
[sagelib-7.4] /usr/include/flint/flint.h: In function 'unsigned int
FLINT_BIT_COUNT(mp_limb_t)':
[sagelib-7.4] /usr/include/flint/flint.h:257:11: error: 'UWtype' was not
declared in this scope
[sagelib-7.4] if (x) count_leading_zeros(zeros, x);
[sagelib-7.4]^
[sagelib-7.4] /usr/include/flint/flint.h:257:11: note: suggested
alternative:
[sagelib-7.4] In file included from /usr/include/recint/ruruint.h:43:0,
[sagelib-7.4]  from /usr/include/recint/rumanip.h:41,
[sagelib-7.4]  from /usr/include/recint/ruconvert.h:43,
[sagelib-7.4]  from /usr/include/gmp++/gmp++_int.h:26,
[sagelib-7.4]  from /usr/include/gmp++/gmp++.h:56,
[sagelib-7.4]  from /usr/include/givaro/givinteger.h:19,
[sagelib-7.4]  from /usr/include/givaro/modular-int8.h:29,
[sagelib-7.4]  from /usr/include/givaro/modular.h:21,
[sagelib-7.4]  from
/«PKGBUILDDIR»/sage/src/build/cythonized/sage/matrix/matrix_modn_dense_double.cpp:532:
[sagelib-7.4] /usr/include/recint/recdefine.h:127:22: note:  
'RecInt::UWtype'
[sagelib-7.4]  typedef uint64_t UWtype;
[sagelib-7.4]   ^~


count_leading_zeros is defined in flints longlong.h. There are several
architecture specific implementations and then in the end this:

#ifndef count_leading_zeros
#define count_leading_zeros(count, x)
...
and similar for count_trailing_zeros.

In our case it seems that count_leading_zeros was already defined in
givaros reclonglong.h so if there is not architecture specific
implementation in longlong.h, the fallback does not work. For the logic
to work we can put in the beginning of longlong.h:

#undef count_leading_zeros
#undef count_trailing_zeros

I didn't test it yet.

Best,
Tobias

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Bug#848799: pcl: FTBFS: make[3]: *** No rule to make target '/usr/lib/libmpi.so', needed by 'lib/x86_64-linux-gnu/libpcl_io.so.1.8.0'. Stop.

2016-12-20 Thread Jochen Sprickerhof 
Control: affects -1 src:gdcm
Control: affects 848793 src:pcl 
Control: merge -1 848793


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Processed (with 1 error): Re: Bug#848799: pcl: FTBFS: make[3]: *** No rule to make target '/usr/lib/libmpi.so', needed by 'lib/x86_64-linux-gnu/libpcl_io.so.1.8.0'. Stop.

2016-12-20 Thread Debian Bug Tracking System 
Processing control commands:

> affects -1 src:gdcm
Bug #848799 [src:vtk6] pcl: FTBFS: make[3]: *** No rule to make target 
'/usr/lib/libmpi.so', needed by 'lib/x86_64-linux-gnu/libpcl_io.so.1.8.0'. Stop.
Added indication that 848799 affects src:gdcm
> affects 848793 src:pcl
Bug #848793 [src:vtk6] gdcm: FTBFS: CMakeFiles/Makefile2:1625: recipe for 
target 'Utilities/VTK/Applications/CMakeFiles/gdcm2pnm.dir/all' failed
Added indication that 848793 affects src:pcl
> merge -1 848793
Bug #848799 [src:vtk6] pcl: FTBFS: make[3]: *** No rule to make target 
'/usr/lib/libmpi.so', needed by 'lib/x86_64-linux-gnu/libpcl_io.so.1.8.0'. Stop.
Unable to merge bugs because:
affects of #848793 is 'src:pcl,src:gdcm' not 'src:gdcm,src:pcl'
Failed to merge 848799: Did not alter merged bugs.


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Re: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

2016-12-20 Thread Sandro Tosi 
> it seems the recent upgrade of numpy has broken some tests in other
> packages like for instance this one in python-skbio.  I wonder whether
> you are either able to suggest patches to get the tests working with the
> new interface of numpy again or whether it might be sensible to revert
> the upgrade of python-numpy to the previous version considering that we
> are quite close to the freeze.

There is still a month to the freeze for the existing package, so
let's not panic already. I'd suggest contacting the upstream of the
projects with failing test and ask for support


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Processed (with 1 error): Re: Bug#848799: pcl: FTBFS: make[3]: *** No rule to make target '/usr/lib/libmpi.so', needed by 'lib/x86_64-linux-gnu/libpcl_io.so.1.8.0'. Stop.

2016-12-20 Thread Debian Bug Tracking System 
Processing control commands:

> reassign -1 src:vtk6
Bug #848799 [src:pcl] pcl: FTBFS: make[3]: *** No rule to make target 
'/usr/lib/libmpi.so', needed by 'lib/x86_64-linux-gnu/libpcl_io.so.1.8.0'. Stop.
Bug reassigned from package 'src:pcl' to 'src:vtk6'.
No longer marked as found in versions pcl/1.8.0+dfsg1-3.
Ignoring request to alter fixed versions of bug #848799 to the same values 
previously set
> affects -1 src:pcl
Bug #848799 [src:vtk6] pcl: FTBFS: make[3]: *** No rule to make target 
'/usr/lib/libmpi.so', needed by 'lib/x86_64-linux-gnu/libpcl_io.so.1.8.0'. Stop.
Added indication that 848799 affects src:pcl
> merge -1 848793
Bug #848799 [src:vtk6] pcl: FTBFS: make[3]: *** No rule to make target 
'/usr/lib/libmpi.so', needed by 'lib/x86_64-linux-gnu/libpcl_io.so.1.8.0'. Stop.
Unable to merge bugs because:
affects of #848793 is 'src:gdcm' not 'src:pcl'
Failed to merge 848799: Did not alter merged bugs.


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Bug#848799: pcl: FTBFS: make[3]: *** No rule to make target '/usr/lib/libmpi.so', needed by 'lib/x86_64-linux-gnu/libpcl_io.so.1.8.0'. Stop.

2016-12-20 Thread Jochen Sprickerhof 
Control: reassign -1 src:vtk6
Control: affects -1 src:pcl
Control: merge -1 848793

Rebuilding should be enough (tested locally).


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Processed: Re: Bug#848793: gdcm: FTBFS: CMakeFiles/Makefile2:1625: recipe for target 'Utilities/VTK/Applications/CMakeFiles/gdcm2pnm.dir/all' failed

2016-12-20 Thread Debian Bug Tracking System 
Processing control commands:

> reassign -1 src:vtk6
Bug #848793 [src:gdcm] gdcm: FTBFS: CMakeFiles/Makefile2:1625: recipe for 
target 'Utilities/VTK/Applications/CMakeFiles/gdcm2pnm.dir/all' failed
Bug reassigned from package 'src:gdcm' to 'src:vtk6'.
No longer marked as found in versions gdcm/2.6.6-3.
Ignoring request to alter fixed versions of bug #848793 to the same values 
previously set
> affects -1 src:gdcm
Bug #848793 [src:vtk6] gdcm: FTBFS: CMakeFiles/Makefile2:1625: recipe for 
target 'Utilities/VTK/Applications/CMakeFiles/gdcm2pnm.dir/all' failed
Added indication that 848793 affects src:gdcm

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Re: r-cran-mcmcpack_1.3-8-1_amd64.changes REJECTED

2016-12-20 Thread Chris Lamb 
Andreas Tille wrote:

> BTW, if I might give some hints about priorities inside new queue from
> the Debian Med perspective besides r-cran-mcmcpack:
> 
>1. libbio-coordinate-perl (helps fixing 2 RC bugs)
>2. r-cran-prettyunits (helps upgrading r-cran-rncl)
>3. r-cran-progress (helps upgrading r-cran-rncl)
>4. camp (helps re-introducing fw4spl and rewards work of newcomer)

Processed. :)


Regards,

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Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

2016-12-20 Thread Andreas Tille 
[Debian Science maintainers and Debian Med packaging in CC as warning]

Hi Sandro,

it seems the recent upgrade of numpy has broken some tests in other
packages like for instance this one in python-skbio.  I wonder whether
you are either able to suggest patches to get the tests working with the
new interface of numpy again or whether it might be sensible to revert
the upgrade of python-numpy to the previous version considering that we
are quite close to the freeze.

Kind regards

Andreas.

On Mon, Dec 19, 2016 at 10:19:10PM +0100, Lucas Nussbaum wrote:
> Source: python-skbio
> Version: 0.5.1-1
> Severity: serious
> Tags: stretch sid
> User: debian...@lists.debian.org
> Usertags: qa-ftbfs-20161219 qa-ftbfs
> Justification: FTBFS on amd64
> 
> Hi,
> 
> During a rebuild of all packages in sid, your package failed to build on
> amd64.
> 
> Relevant part (hopefully):
> > multiple_comparisons_correction=None)
> >   File 
> > "/<>/.pybuild/pythonX.Y_3.5/build/skbio/stats/composition.py", 
> > line 971, in ancom
> > _logratio_mat = _log_compare(mat.values, cats.values, significance_test)
> >   File 
> > "/<>/.pybuild/pythonX.Y_3.5/build/skbio/stats/composition.py", 
> > line 1084, in _log_compare
> > arr=ratio)
> >   File "/usr/lib/python3/dist-packages/numpy/lib/shape_base.py", line 133, 
> > in apply_along_axis
> > if res.shape == ():
> > AttributeError: 'F_onewayResult' object has no attribute 'shape'
> > 
> > --
> > Ran 2238 tests in 42.139s
> > 
> > FAILED (SKIP=30, errors=15)
> > E: pybuild pybuild:276: test: plugin distutils failed with: exit code=1: cd 
> > /<>/.pybuild/pythonX.Y_3.5/build; python3.5 -m nose 
> > dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.5 returned 
> > exit code 13
> > debian/rules:22: recipe for target 'override_dh_auto_test' failed
> 
> The full build log is available from:
>http://aws-logs.debian.net/2016/12/19/python-skbio_0.5.1-1_unstable.log
> 
> A list of current common problems and possible solutions is available at
> http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
> 
> About the archive rebuild: The rebuild was done on EC2 VM instances from
> Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
> failed build was retried once to eliminate random failures.
> 
> ___
> Debian-med-packaging mailing list
> debian-med-packag...@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
> 

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