Bug#894559: petsc: FTBFS against hypre 2.14

[Drew Parsons]

Source: petsc
Version: 3.8.4+dfsg1-1
Severity: normal

petsc 3.8.4 fails to build against hypre 2.14, which is in experimental.

Upstream has already patched,
https://bitbucket.org/petsc/petsc/commits/e6de09342ce9c4562cc062ff2c1bac4bd956bda0

This is just a tracker bug to inform the hypre upgrade.  Either wait
for the next PETSc release, or apply the patch.


-- System Information:
Debian Release: buster/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.15.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), 
LANGUAGE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

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Accepted petsc 3.8.4+dfsg1-1 (source amd64 all) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sun, 01 Apr 2018 17:59:27 +0800
Source: petsc
Binary: libpetsc-real3.8-dev petsc-dev libpetsc-real3.8 libpetsc-real3.8-dbg 
petsc3.8-doc libpetsc-complex3.8-dev libpetsc-complex3.8 libpetsc-complex3.8-dbg
Architecture: source amd64 all
Version: 3.8.4+dfsg1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 libpetsc-complex3.8 - Shared libraries for version 3.8 of PETSc with Complex 
Numbers
 libpetsc-complex3.8-dbg - Debugging libraries for PETSc
 libpetsc-complex3.8-dev - Static libraries, shared links, header files for 
PETSc
 libpetsc-real3.8 - Shared libraries for version 3.8 of PETSc
 libpetsc-real3.8-dbg - Debugging libraries for PETSc
 libpetsc-real3.8-dev - Static libraries, shared links, header files for PETSc
 petsc-dev  - Virtual package depending on latest PETSc development package
 petsc3.8-doc - Documentation and examples for PETSc
Changes:
 petsc (3.8.4+dfsg1-1) unstable; urgency=medium
 .
   * New upstream release.
   * debian/control: change Vcs-Git to https so general users can clone.
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Accepted hypre 2.14.0-1exp1 (source amd64) into experimental, experimental

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Tue, 27 Mar 2018 14:05:07 +0800
Source: hypre
Binary: libhypre-2.14.0 libhypre-dev
Architecture: source amd64
Version: 2.14.0-1exp1
Distribution: experimental
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 libhypre-2.14.0 - High Performance Matrix Preconditioners - Shared Library
 libhypre-dev - High Performance Matrix Preconditioners - Development Files
Changes:
 hypre (2.14.0-1exp1) experimental; urgency=medium
 .
   * Team upload.
   * New upstream version 2.14.0
 - new AIR AMG solver
 - refresh debian patches, add superlu_libs.patch to link against
   libsuper_dist.so
   * d/rules: read upstream version from debian/changelog
   * Standards-Version: 4.1.3
   * debhelper compatibility level 11
   * update VCS tags to salsa.debian.org
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Accepted petsc4py 3.8.1-3 (source) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 21 Mar 2018 09:26:49 +0800
Source: petsc4py
Binary: python-petsc4py python3-petsc4py python-petsc4py-docs
Architecture: source
Version: 3.8.1-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 python-petsc4py - Python 2 bindings for PETSc libraries
 python-petsc4py-docs - Python bindings for PETSc libraries: documentation and 
examples
 python3-petsc4py - Python 3 bindings for PETSc libraries
Closes: 893653
Changes:
 petsc4py (3.8.1-3) unstable; urgency=medium
 .
   * update VCS tags to salsa.debian.org
   * d/rules: update path to PETSc*.so to remove RUNPATH (python build
 infrastructure has changed). Closes: #893653.
   * Build-Depends: python3-distutils
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Accepted slepc 3.8.2+dfsg1-4 (source) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 21 Mar 2018 02:09:13 +0800
Source: slepc
Binary: slepc-dev libslepc-real3.8-dev libslepc-real3.8 slepc3.8-doc 
libslepc-complex3.8-dev libslepc-complex3.8
Architecture: source
Version: 3.8.2+dfsg1-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 libslepc-complex3.8 - Scalable Library for Eigenvalue Problem Computations
 libslepc-complex3.8-dev - Scalable Library for Eigenvalue Problem Computations
 libslepc-real3.8 - Scalable Library for Eigenvalue Problem Computations
 libslepc-real3.8-dev - Scalable Library for Eigenvalue Problem Computations
 slepc-dev  - Scalable Library for Eigenvalue Problem Computations
 slepc3.8-doc - Scalable Library for Eigenvalue Problem Computations
Changes:
 slepc (3.8.2+dfsg1-4) unstable; urgency=medium
 .
   * debian patch install_slepcconf.h_SLEPC_DIR-25fa25f10d6.diff
 applies upstream commit 25fa25f10d6 to fix value of SLEPC_DIR in
 slepcconf.h.
   * debian/control: update VCS tags to salsa.debian.org
   * debian patch make_parallel_47f9c11.patch applies upstream commit
 47f9c11 to facilitate parallel builds.
   * don't install lib/slepc/conf/uninstall.py into dev packages.
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Accepted petsc 3.8.3+dfsg1-7 (source) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 21 Mar 2018 00:59:49 +0800
Source: petsc
Binary: libpetsc-real3.8-dev petsc-dev libpetsc-real3.8 libpetsc-real3.8-dbg 
petsc3.8-doc libpetsc-complex3.8-dev libpetsc-complex3.8 libpetsc-complex3.8-dbg
Architecture: source
Version: 3.8.3+dfsg1-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 libpetsc-complex3.8 - Shared libraries for version 3.8 of PETSc with Complex 
Numbers
 libpetsc-complex3.8-dbg - Debugging libraries for PETSc
 libpetsc-complex3.8-dev - Static libraries, shared links, header files for 
PETSc
 libpetsc-real3.8 - Shared libraries for version 3.8 of PETSc
 libpetsc-real3.8-dbg - Debugging libraries for PETSc
 libpetsc-real3.8-dev - Static libraries, shared links, header files for PETSc
 petsc-dev  - Virtual package depending on latest PETSc development package
 petsc3.8-doc - Documentation and examples for PETSc
Closes: 893509
Changes:
 petsc (3.8.3+dfsg1-7) unstable; urgency=medium
 .
   * debian patch make_parallel_f88a919.patch, adapted from upstream
 merge f88a919 to facilitate parallel builds. Closes: #893509.
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Accepted petsc 3.8.3+dfsg1-6 (source) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Mon, 19 Mar 2018 14:27:45 +0800
Source: petsc
Binary: libpetsc-real3.8-dev petsc-dev libpetsc-real3.8 libpetsc-real3.8-dbg 
petsc3.8-doc libpetsc-complex3.8-dev libpetsc-complex3.8 libpetsc-complex3.8-dbg
Architecture: source
Version: 3.8.3+dfsg1-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 libpetsc-complex3.8 - Shared libraries for version 3.8 of PETSc with Complex 
Numbers
 libpetsc-complex3.8-dbg - Debugging libraries for PETSc
 libpetsc-complex3.8-dev - Static libraries, shared links, header files for 
PETSc
 libpetsc-real3.8 - Shared libraries for version 3.8 of PETSc
 libpetsc-real3.8-dbg - Debugging libraries for PETSc
 libpetsc-real3.8-dev - Static libraries, shared links, header files for PETSc
 petsc-dev  - Virtual package depending on latest PETSc development package
 petsc3.8-doc - Documentation and examples for PETSc
Changes:
 petsc (3.8.3+dfsg1-6) unstable; urgency=medium
 .
   * use upstream patches b1eb7ee26db and deb554b to fix PETSC_DIR in
 petscconf.h.
   * update VCS tags to salsa.debian.org
   * debian/rules: define DEB_STRIPPED_UPSTREAM_VERSION as upstream
 version (regardless of whether we applied dfsg or not)
   * don't write the build dir (-fdebug-prefix-map) into the installed
 configuration files
   * don't install conf/uninstall.py
   * d/rules: use DEB_BUILD_OPTIONS to set the number of cpus (nproc)
 available for a parallel build (parallel=`nproc`)
   * debhelper compatibility level 11
   * Standards-Version: 4.1.3
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Bug#892797: sasview: should look for data files in home dir not package dir

[Drew Parsons]

On Tue, 13 Mar 2018 13:00:52 +0800 Drew Parsons <dpars...@debian.org>
wrote:
> 
> Of course no data files will be found there.  The dialog should be
> configured to start from the user's home dir (or recently used, or
> somesuch).
> 

It's likely somewhere in the wxPython API, around wx.FileDialog, 
cf. ll.352,357 in sas/sasgui/guiframe/gui_manager.py

https://docs.wxpython.org/wx.FileDialog.html#wx.FileDialog
We probably want to set defaultDir to os.path.expanduser("~") in the
constructor.  Extra marks for not doing that if a "recent dir" is
available instead, e.g check dlg.GetDirectory() and only SetDirectory
expanduser("~") if it's empty.


Drew

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Bug#892797: sasview: should look for data files in home dir not package dir

[Drew Parsons]

Package: sasview
Version: 4.2.0~git20180309-2
Severity: normal

Currently when using the gui interface to open a new data file, the
"Choose a file" dialog window starts from the package directory, 
/usr/lib/python2.7/dist-packages/sas/sasview.

Of course no data files will be found there.  The dialog should be
configured to start from the user's home dir (or recently used, or
somesuch).



-- System Information:
Debian Release: buster/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.15.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), 
LANGUAGE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages sasview depends on:
ii  python2.7.14-4
ii  python-numpy  1:1.13.3-2
ii  python-pkg-resources  38.5.2-1
ii  python-sasview4.2.0~git20180309-2

sasview recommends no packages.

Versions of packages sasview suggests:
ii  sasview-doc  4.2.0~git20180309-2

-- no debconf information

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Accepted petsc 3.8.3+dfsg1-5 (source) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Mon, 05 Mar 2018 02:53:44 +0800
Source: petsc
Binary: libpetsc-real3.8-dev petsc-dev libpetsc-real3.8 libpetsc-real3.8-dbg 
petsc3.8-doc libpetsc-complex3.8-dev libpetsc-complex3.8 libpetsc-complex3.8-dbg
Architecture: source
Version: 3.8.3+dfsg1-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 libpetsc-complex3.8 - Shared libraries for version 3.8 of PETSc with Complex 
Numbers
 libpetsc-complex3.8-dbg - Debugging libraries for PETSc
 libpetsc-complex3.8-dev - Static libraries, shared links, header files for 
PETSc
 libpetsc-real3.8 - Shared libraries for version 3.8 of PETSc
 libpetsc-real3.8-dbg - Debugging libraries for PETSc
 libpetsc-real3.8-dev - Static libraries, shared links, header files for PETSc
 petsc-dev  - Virtual package depending on latest PETSc development package
 petsc3.8-doc - Documentation and examples for PETSc
Changes:
 petsc (3.8.3+dfsg1-5) unstable; urgency=medium
 .
   * debian/extract_MPI_dependency: handle alpha/beta markers in minor
 version. e.g. take mpich 3.3~a2 as >= 3.3~a2, << 3.4.
   * debian/rules: create a blacklist for arches known to fail tests on
 the build daemons. Build them without running tests.
 Currently ARCH_NO_TEST_LIST=powerpc x32
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Accepted dolfin 2017.2.0.post0-3 (source) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sun, 04 Mar 2018 10:46:39 +0800
Source: dolfin
Binary: libdolfin-dev libdolfin2017.2 python-dolfin python3-dolfin dolfin-doc 
dolfin-bin
Architecture: source
Version: 2017.2.0.post0-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Team 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 dolfin-bin - Executable scripts for DOLFIN
 dolfin-doc - Documentation and demo programs for DOLFIN
 libdolfin-dev - Shared links and header files for DOLFIN
 libdolfin2017.2 - Shared libraries for DOLFIN
 python-dolfin - Python interface for DOLFIN (Python 2)
 python3-dolfin - Python interface for DOLFIN (Python 3)
Changes:
 dolfin (2017.2.0.post0-3) unstable; urgency=medium
 .
   * update petsc/slepc dependencies for PETSc/SLEPc 3.8
 (dev package now libpetsc-real3.8-dev not libpetsc3.8.3-dev)
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Accepted slepc4py 3.8.0-2 (source) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sun, 04 Mar 2018 00:50:46 +0800
Source: slepc4py
Binary: python-slepc4py python3-slepc4py python-slepc4py-docs
Architecture: source
Version: 3.8.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 python-slepc4py - Python 2 bindings for SLEPc libraries
 python-slepc4py-docs - Python bindings for SLEPc libraries: documentation and 
examples
 python3-slepc4py - Python 3 bindings for SLEPc libraries
Changes:
 slepc4py (3.8.0-2) unstable; urgency=medium
 .
   * debian/rules: automatically read version (3.8) from changelog
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Accepted petsc 3.8.3+dfsg1-4 (source) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sat, 03 Mar 2018 16:37:58 +0800
Source: petsc
Binary: libpetsc-real3.8-dev petsc-dev libpetsc-real3.8 libpetsc-real3.8-dbg 
petsc3.8-doc libpetsc-complex3.8-dev libpetsc-complex3.8 libpetsc-complex3.8-dbg
Architecture: source
Version: 3.8.3+dfsg1-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 libpetsc-complex3.8 - Shared libraries for version 3.8 of PETSc with Complex 
Numbers
 libpetsc-complex3.8-dbg - Debugging libraries for PETSc
 libpetsc-complex3.8-dev - Static libraries, shared links, header files for 
PETSc
 libpetsc-real3.8 - Shared libraries for version 3.8 of PETSc
 libpetsc-real3.8-dbg - Debugging libraries for PETSc
 libpetsc-real3.8-dev - Static libraries, shared links, header files for PETSc
 petsc-dev  - Virtual package depending on latest PETSc development package
 petsc3.8-doc - Documentation and examples for PETSc
Changes:
 petsc (3.8.3+dfsg1-4) unstable; urgency=medium
 .
   * debian/rules: separate -arch and -indep rules for
 override_dh_auto_install. Fixing petscconf.h applies to -arch only.
Checksums-Sha1:
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petsc_3.8.3+dfsg1-4.debian.tar.xz
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petsc_3.8.3+dfsg1-4.debian.tar.xz
Files:
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petsc_3.8.3+dfsg1-4.debian.tar.xz

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Accepted slepc 3.8.2+dfsg1-3 (source) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sat, 03 Mar 2018 15:59:15 +0800
Source: slepc
Binary: slepc-dev libslepc-real3.8-dev libslepc-real3.8 slepc3.8-doc 
libslepc-complex3.8-dev libslepc-complex3.8
Architecture: source
Version: 3.8.2+dfsg1-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 libslepc-complex3.8 - Scalable Library for Eigenvalue Problem Computations
 libslepc-complex3.8-dev - Scalable Library for Eigenvalue Problem Computations
 libslepc-real3.8 - Scalable Library for Eigenvalue Problem Computations
 libslepc-real3.8-dev - Scalable Library for Eigenvalue Problem Computations
 slepc-dev  - Scalable Library for Eigenvalue Problem Computations
 slepc3.8-doc - Scalable Library for Eigenvalue Problem Computations
Changes:
 slepc (3.8.2+dfsg1-3) unstable; urgency=medium
 .
   * debian/rules: separate -arch and -indep rules for
 override_dh_auto_install. Fixing slepcconf.h applies to -arch.
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slepc_3.8.2+dfsg1-3.debian.tar.xz
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slepc_3.8.2+dfsg1-3.debian.tar.xz

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Accepted petsc 3.8.3+dfsg1-3 (source) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sat, 03 Mar 2018 11:59:03 +0800
Source: petsc
Binary: libpetsc-real3.8-dev petsc-dev libpetsc-real3.8 libpetsc-real3.8-dbg 
petsc3.8-doc libpetsc-complex3.8-dev libpetsc-complex3.8 libpetsc-complex3.8-dbg
Architecture: source
Version: 3.8.3+dfsg1-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 libpetsc-complex3.8 - Shared libraries for version 3.8 of PETSc with Complex 
Numbers
 libpetsc-complex3.8-dbg - Debugging libraries for PETSc
 libpetsc-complex3.8-dev - Static libraries, shared links, header files for 
PETSc
 libpetsc-real3.8 - Shared libraries for version 3.8 of PETSc
 libpetsc-real3.8-dbg - Debugging libraries for PETSc
 libpetsc-real3.8-dev - Static libraries, shared links, header files for PETSc
 petsc-dev  - Virtual package depending on latest PETSc development package
 petsc3.8-doc - Documentation and examples for PETSc
Closes: 891952
Changes:
 petsc (3.8.3+dfsg1-3) unstable; urgency=medium
 .
   * set PETSC_DIR in petscconf.h to install dir not build dir.
 Closes: #891952.
Checksums-Sha1:
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petsc_3.8.3+dfsg1-3.debian.tar.xz
Files:
 bcca4a8b5553d89dc69ecc747750b510 3022 devel optional petsc_3.8.3+dfsg1-3.dsc
 97f2cda1ff8450960cc54c3c1bc751c4 36484 devel optional 
petsc_3.8.3+dfsg1-3.debian.tar.xz

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Accepted slepc 3.8.2+dfsg1-2 (source) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sat, 03 Mar 2018 11:34:18 +0800
Source: slepc
Binary: slepc-dev libslepc-real3.8-dev libslepc-real3.8 slepc3.8-doc 
libslepc-complex3.8-dev libslepc-complex3.8
Architecture: source
Version: 3.8.2+dfsg1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 libslepc-complex3.8 - Scalable Library for Eigenvalue Problem Computations
 libslepc-complex3.8-dev - Scalable Library for Eigenvalue Problem Computations
 libslepc-real3.8 - Scalable Library for Eigenvalue Problem Computations
 libslepc-real3.8-dev - Scalable Library for Eigenvalue Problem Computations
 slepc-dev  - Scalable Library for Eigenvalue Problem Computations
 slepc3.8-doc - Scalable Library for Eigenvalue Problem Computations
Closes: 891775
Changes:
 slepc (3.8.2+dfsg1-2) unstable; urgency=medium
 .
   * set SLEPC_DIR in slepcconf.h to install dir not build dir.
 Closes: #891775.
Checksums-Sha1:
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slepc_3.8.2+dfsg1-2.debian.tar.xz
Files:
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 0d33203153288437ab2e9e73b8e56452 15088 libs optional 
slepc_3.8.2+dfsg1-2.debian.tar.xz

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Accepted petsc4py 3.8.1-2 (source) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sat, 03 Mar 2018 09:06:33 +0800
Source: petsc4py
Binary: python-petsc4py python3-petsc4py python-petsc4py-docs
Architecture: source
Version: 3.8.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 python-petsc4py - Python 2 bindings for PETSc libraries
 python-petsc4py-docs - Python bindings for PETSc libraries: documentation and 
examples
 python3-petsc4py - Python 3 bindings for PETSc libraries
Changes:
 petsc4py (3.8.1-2) unstable; urgency=medium
 .
   * Standards-Version: 4.1.3
   * debhelper compatibility level 11
Checksums-Sha1:
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Checksums-Sha256:
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 01b16cb42dab674ffee29eaf45dbafcbd01709353b655e48c102f5c1fb015bb0 6440 
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Files:
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 bfbffca0ca6b5529f6439a99af3fbee8 6440 python optional 
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Accepted petsc 3.8.3+dfsg1-2 (source) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Tue, 27 Feb 2018 08:30:06 +0800
Source: petsc
Binary: libpetsc-real3.8-dev petsc-dev libpetsc-real3.8 libpetsc-real3.8-dbg 
petsc3.8-doc libpetsc-complex3.8-dev libpetsc-complex3.8 libpetsc-complex3.8-dbg
Architecture: source
Version: 3.8.3+dfsg1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 libpetsc-complex3.8 - Shared libraries for version 3.8 of PETSc with Complex 
Numbers
 libpetsc-complex3.8-dbg - Debugging libraries for PETSc
 libpetsc-complex3.8-dev - Static libraries, shared links, header files for 
PETSc
 libpetsc-real3.8 - Shared libraries for version 3.8 of PETSc
 libpetsc-real3.8-dbg - Debugging libraries for PETSc
 libpetsc-real3.8-dev - Static libraries, shared links, header files for PETSc
 petsc-dev  - Virtual package depending on latest PETSc development package
 petsc3.8-doc - Documentation and examples for PETSc
Changes:
 petsc (3.8.3+dfsg1-2) unstable; urgency=medium
 .
   * drop Recommends: csh (petscmpiexec now converted to posix)
Checksums-Sha1:
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petsc_3.8.3+dfsg1-2.debian.tar.xz
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petsc_3.8.3+dfsg1-2.dsc
 4255a46c9ff757582ae71be76b8b3742828ce82fa743267ebb0cd9614e485c8b 36384 
petsc_3.8.3+dfsg1-2.debian.tar.xz
Files:
 e8fdf5c31adaebe82c30ce5417de0a7a 3022 devel optional petsc_3.8.3+dfsg1-2.dsc
 a01c275e16d8e12c09ad3ed0e20551b7 36384 devel optional 
petsc_3.8.3+dfsg1-2.debian.tar.xz

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Bug#891775: libslepc3.7-dev: SLEPC_DIR in slepcconf.h refers to builddir not installdir

[Drew Parsons]

Package: libslepc3.7-dev
Version: 3.7.4+dfsg1-2+b5
Severity: normal

slepcconf.h is generated at build time and installed in the include
directory.

It contains a definition of SLEPC_DIR, which currently is populated
with the builddir.  It should instead refer to the installdir (as used
for SLEPC_LIB_DIR in the same file)


-- System Information:
Debian Release: buster/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.15.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), 
LANGUAGE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages libslepc3.7-dev depends on:
ii  libslepc3.7.4-dev  3.7.4+dfsg1-2+b5

libslepc3.7-dev recommends no packages.

libslepc3.7-dev suggests no packages.

-- no debconf information

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Accepted slepc 3.8.2+dfsg1-1exp3 (source amd64 all) into experimental

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Thu, 01 Mar 2018 01:40:00 +0800
Source: slepc
Binary: slepc-dev libslepc-real3.8-dev libslepc-real3.8 slepc3.8-doc 
libslepc-complex3.8-dev libslepc-complex3.8
Architecture: source amd64 all
Version: 3.8.2+dfsg1-1exp3
Distribution: experimental
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 libslepc-complex3.8 - Scalable Library for Eigenvalue Problem Computations
 libslepc-complex3.8-dev - Scalable Library for Eigenvalue Problem Computations
 libslepc-real3.8 - Scalable Library for Eigenvalue Problem Computations
 libslepc-real3.8-dev - Scalable Library for Eigenvalue Problem Computations
 slepc-dev  - Scalable Library for Eigenvalue Problem Computations
 slepc3.8-doc - Scalable Library for Eigenvalue Problem Computations
Changes:
 slepc (3.8.2+dfsg1-1exp3) experimental; urgency=medium
 .
   * Refresh i386 patch as slepcmath_xmmintrin_MM_FLUSH_ZERO_i386.patch,
 testing for __SSE__.  Flush To Zero was introduced with SSE in
 1999 on the Pentium III. Thanks Jose Roman for the updated patch.
Checksums-Sha1:
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slepc_3.8.2+dfsg1-1exp3.debian.tar.xz
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libslepc-real3.8_3.8.2+dfsg1-1exp3_amd64.deb
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slepc-dev_3.8.2+dfsg1-1exp3_amd64.deb
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slepc3.8-doc_3.8.2+dfsg1-1exp3_all.deb
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Checksums-Sha256:
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slepc_3.8.2+dfsg1-1exp3.debian.tar.xz
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libslepc-complex3.8-dev_3.8.2+dfsg1-1exp3_amd64.deb
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libslepc-complex3.8_3.8.2+dfsg1-1exp3_amd64.deb
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libslepc-real3.8-dbgsym_3.8.2+dfsg1-1exp3_amd64.deb
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libslepc-real3.8-dev_3.8.2+dfsg1-1exp3_amd64.deb
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libslepc-real3.8_3.8.2+dfsg1-1exp3_amd64.deb
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slepc-dev_3.8.2+dfsg1-1exp3_amd64.deb
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slepc3.8-doc_3.8.2+dfsg1-1exp3_all.deb
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Accepted slepc4py 3.8.0-1exp2 (source amd64 all) into experimental

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 28 Feb 2018 17:10:20 +0800
Source: slepc4py
Binary: python-slepc4py python3-slepc4py python-slepc4py-docs
Architecture: source amd64 all
Version: 3.8.0-1exp2
Distribution: experimental
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 python-slepc4py - Python 2 bindings for SLEPc libraries
 python-slepc4py-docs - Python bindings for SLEPc libraries: documentation and 
examples
 python3-slepc4py - Python 3 bindings for SLEPc libraries
Changes:
 slepc4py (3.8.0-1exp2) experimental; urgency=medium
 .
   * debian/rules: the dh_installdocs override applies to build-indep
 only (otherwise, building build-arch only fails)
   * Standards-Version: 4.1.3
   * debhelper compatibility level 11
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 67ca7d9bb659b9426fb997aa4c51e720775761cdc0d1b397ac8398272424e517 11480 
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python-slepc4py-dbgsym_3.8.0-1exp2_amd64.deb
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python-slepc4py-docs_3.8.0-1exp2_all.deb
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python-slepc4py_3.8.0-1exp2_amd64.deb
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python3-slepc4py-dbgsym_3.8.0-1exp2_amd64.deb
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python3-slepc4py_3.8.0-1exp2_amd64.deb
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slepc4py_3.8.0-1exp2_amd64.buildinfo

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Accepted petsc4py 3.8.1-1exp2 (source amd64 all) into experimental

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Tue, 27 Feb 2018 16:55:02 +0800
Source: petsc4py
Binary: python-petsc4py python3-petsc4py python-petsc4py-docs
Architecture: source amd64 all
Version: 3.8.1-1exp2
Distribution: experimental
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 python-petsc4py - Python 2 bindings for PETSc libraries
 python-petsc4py-docs - Python bindings for PETSc libraries: documentation and 
examples
 python3-petsc4py - Python 3 bindings for PETSc libraries
Changes:
 petsc4py (3.8.1-1exp2) experimental; urgency=medium
 .
   * debian/rules: the dh_installdocs override applies to build-indep
 only (otherwise, building build-arch only fails)
Checksums-Sha1:
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python3-petsc4py_3.8.1-1exp2_amd64.deb
Files:
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petsc4py_3.8.1-1exp2.debian.tar.xz
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petsc4py_3.8.1-1exp2_amd64.buildinfo
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python-petsc4py-dbgsym_3.8.1-1exp2_amd64.deb
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python-petsc4py-docs_3.8.1-1exp2_all.deb
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python-petsc4py_3.8.1-1exp2_amd64.deb
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python3-petsc4py-dbgsym_3.8.1-1exp2_amd64.deb
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python3-petsc4py_3.8.1-1exp2_amd64.deb

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Accepted slepc 3.8.2+dfsg1-1exp1 (source amd64 all) into experimental

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Tue, 27 Feb 2018 15:39:06 +0800
Source: slepc
Binary: slepc-dev libslepc-real3.8-dev libslepc-real3.8 slepc3.8-doc 
libslepc-complex3.8-dev libslepc-complex3.8
Architecture: source amd64 all
Version: 3.8.2+dfsg1-1exp1
Distribution: experimental
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 libslepc-complex3.8 - Scalable Library for Eigenvalue Problem Computations
 libslepc-complex3.8-dev - Scalable Library for Eigenvalue Problem Computations
 libslepc-real3.8 - Scalable Library for Eigenvalue Problem Computations
 libslepc-real3.8-dev - Scalable Library for Eigenvalue Problem Computations
 slepc-dev  - Scalable Library for Eigenvalue Problem Computations
 slepc3.8-doc - Scalable Library for Eigenvalue Problem Computations
Changes:
 slepc (3.8.2+dfsg1-1exp1) experimental; urgency=medium
 .
   * New upstream version.
   * Standards-Version: 4.1.3
   * debhelper compatibility level 11
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libslepc-real3.8_3.8.2+dfsg1-1exp1_amd64.deb
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slepc_3.8.2+dfsg1-1exp1_amd64.buildinfo

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Accepted petsc4py 3.8.1-1exp1 (source amd64 all) into experimental

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Tue, 27 Feb 2018 10:48:11 +0800
Source: petsc4py
Binary: python-petsc4py python3-petsc4py python-petsc4py-docs
Architecture: source amd64 all
Version: 3.8.1-1exp1
Distribution: experimental
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 python-petsc4py - Python 2 bindings for PETSc libraries
 python-petsc4py-docs - Python bindings for PETSc libraries: documentation and 
examples
 python3-petsc4py - Python 3 bindings for PETSc libraries
Changes:
 petsc4py (3.8.1-1exp1) experimental; urgency=medium
 .
   * New upstream version.
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petsc4py_3.8.1-1exp1_amd64.buildinfo
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python-petsc4py-dbgsym_3.8.1-1exp1_amd64.deb
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python-petsc4py-docs_3.8.1-1exp1_all.deb
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python3-petsc4py_3.8.1-1exp1_amd64.deb

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Accepted petsc 3.8.0+dfsg1-1exp1 (source amd64 all) into experimental, experimental

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Fri, 03 Nov 2017 09:36:28 +0800
Source: petsc
Binary: libpetsc-real3.8-dev petsc-dev libpetsc-real3.8 libpetsc-real3.8-dbg 
petsc3.8-doc libpetsc-complex3.8-dev libpetsc-complex3.8 libpetsc-complex3.8-dbg
Architecture: source amd64 all
Version: 3.8.0+dfsg1-1exp1
Distribution: experimental
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 libpetsc-complex3.8 - Shared libraries for version 3.8 of PETSc with Complex 
Numbers
 libpetsc-complex3.8-dbg - Debugging libraries for PETSc
 libpetsc-complex3.8-dev - Static libraries, shared links, header files for 
PETSc
 libpetsc-real3.8 - Shared libraries for version 3.8 of PETSc
 libpetsc-real3.8-dbg - Debugging libraries for PETSc
 libpetsc-real3.8-dev - Static libraries, shared links, header files for PETSc
 petsc-dev  - Virtual package depending on latest PETSc development package
 petsc3.8-doc - Documentation and examples for PETSc
Changes:
 petsc (3.8.0+dfsg1-1exp1) experimental; urgency=medium
 .
   * Team upload.
   * New upstream version.
 - updated API, fortran interfaces are simplified.
   * Remove deprecated debian patches:
 - applied upstream:
 build-ssl1.1.patch
 mpi-version-test.patch
 g++-4.8.patch
 - redundant:
 example-src-dir.patch
 install-dir.patch
 configure-kfreebsd8.patch
   * New package structure: drop patch-specific versions and alternatives
 i.e. drop 3.8.0 specific packages, any 3.8.Z will satisfy petsc3.8
   * configuration updates:
 - configure option --with-mpi-dir not required
   (specify MPI compilers mpicc,mpicxx,mpif90 explicitly)
 - use pkg-config to set hdf5 include and libs
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petsc-dev_3.8.0+dfsg1-1exp1_all.deb
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petsc3.8-doc_3.8.0+dfsg1-1exp1_all.deb
 d5f666a48d16805963d81ceb46d6a1902ceb434fd5dd1c14df9051b5fd5c13f0 10959 
petsc_3.8.0+dfsg1-1exp1_amd64.buildinfo
Files:
 98aac88591606dc13488d8d662932100 2913 devel optional 
petsc_3.8.0+dfsg1-1exp1.dsc
 621e08688e08bb80a0107d5e671cdae9 24604815 devel optional 
petsc_3.8.0+dfsg1.orig.tar.gz
 453477e0c530572695c670ca98a35e12 34476 devel optional 
petsc_3.8.0+dfsg1-1exp1.debian.tar.xz
 aebb5251f1fb6dfa5aff75d6174825c3 20792660 debug optional 
libpetsc-complex3.8-dbg_3.8.0+dfsg1-1exp1_amd64.deb
 4de568c1513951c1cd30f8e4506faec5 7920728 libdevel optional 
libpetsc-complex3.8-dev_3.8.0+dfsg1-1exp1_amd64.deb
 db193486927f987d28008639d358c165 4373132 libs optional 
libpetsc-complex3.8_3.8.0+dfsg1-1ex

Re: Comments regarding petsc_3.8.0+dfsg1-1exp1_amd64.changes

[Drew Parsons]

On Sat, 2018-02-24 at 16:07 +, Thorsten Alteholz wrote:
> Hi Drew,
> 
> one of our trainess had a look at your package and found the
> following 
> stuff. He is nice and doesn't want to reject the package but just
> have
> your comments :-).
> 
> Thanks!
>  Thorsten
> 

Thanks Thorsten.


> 
> Not lintian-clean:
>  * package-has-unnecessary-activation-of-ldconfig-trigger (1)

This seems to be a lintian bug (the detailed message for the warning
says so).  There's nothing in debian/rules that explicitly invoke
ldconfig.


>  * csh-considered-harmful (1)

Annoying to edit upstream scripts, so I haven't bothered much with
them. But in the long run it's probably good for them if we do.  These
are auxiliary utility scripts, not routinely used. Most programs would
use PETsc via the C++ API instead (or petsc4py for python)

>  * executable-not-elf-or-script (37)

matlab scripts.  Not sure why upstream marks them as executable.  I
guess it's not needed, I can remove the executable flag.

> Format in d/copyright is in http, where https is prefered.
> 
> I'm not sure whether it is possible to reproduce the following files
> (and
> whether is is required at all):
> 
> - petsc-3.8.0/share/petsc/datafiles/matrices/ contain suspicious
> files in binary
>   format. Quite possible related to some computational stuff, but i'm
> not sure.

These are example matrices used by
petsc/matlab/generatePetscTestFiles.m to test the matlab interface to
PETSc.


> - petsc-3.8.0/share/petsc/datafiles/meshes/*.exo are in CDF format,
> which is
>   rather a binary format.
> 
> - petsc-3.8.0/share/petsc/datafiles/meshes/*.med are in HDF format,
> which is
>   rather a binary format.
> 
> - petsc-3.8.0/share/petsc/datafiles/meshes/*.cgns are in ADF format,
> which is
>   rather a binary format for database storing.
> 
> - petsc-3.8.0/share/petsc/datafiles/meshes/horse.ply.bz2 is an
> archived file,
>   containing some binary data.
> 
> - petsc-
3.8.0/petsc/src/dm/impls/moab/examples/tests/input/ex3_in.h5m 
> is a
>  
 binary file in HDF format.

These are data files and meshes defining the geometries of various 2D
and 3D objects provided for use in examples and tests.The tests and
examples that use them are located below 
/usr/lib/petscdir/petsc3.8/x86_64-linux-gnu-real/share/petsc/examples/src/
(there are different tests for the various PETSc components)

You can view the .exo fils in paraview, 
and also the horse.ply after decompressing.  

gmsh shows you the mesh in the .msh and .med files.

cgns is a format used by some computational fluid dynamics software.
The cgns library is in debian. You can view and plot using cgnsview.



> 
> - petsc-3.8.0/petsc/src/dm/impls/moab/examples/tests/input/ex3_in.h5m 
> is a
> binary file in HDF format.

dm/impls/moab's ex3 test generates a h5m file (when its -io option is
used).  I think input/ex3_in.h5m is a record of what it is supposed to
generate, which could be used to confirm that PETSc is working
correctly. You can inspect the contents using HDFCompass.  HDF5 is a
general file format for storing complex datasets.  It's very general,
so you organise your data according to your needs using your own
schema.  h5m is Moab's HDF5 file format, using their own schema to
store data in an hdf5 file,
https://www.mcs.anl.gov/~fathom/moab-docs/h5mmain.html
It's used to store finite element mesh information (vertices and
connectivity, geometry and topology).  We don't have moab in debian but
it's LGPL (https://bitbucket.org/fathomteam/moab/src), so we couldpackage it, 
if anyone really wants to check what's in 
petsc/src/dm/impls/moab/examples/tests/input/ex3_in.h5m



> Also d/copyritgh is not full. I've found the following file:
> 
> petsc-3.8.0/src/ksp/ksp/examples/tutorials/ex63.cxx, which is
> licensed under
> BSD-2-clause and copyrighted 2011 Sandia, but it is absent from
> d/copyright.

Thanks, I'll update copyright.

Drew




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Accepted dolfin 2017.2.0.post0-2 (source) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
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Format: 1.8
Date: Thu, 22 Feb 2018 08:56:02 +0800
Source: dolfin
Binary: libdolfin-dev libdolfin2017.2 python-dolfin python3-dolfin dolfin-doc 
dolfin-bin
Architecture: source
Version: 2017.2.0.post0-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Team 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 dolfin-bin - Executable scripts for DOLFIN
 dolfin-doc - Documentation and demo programs for DOLFIN
 libdolfin-dev - Shared links and header files for DOLFIN
 libdolfin2017.2 - Shared libraries for DOLFIN
 python-dolfin - Python interface for DOLFIN (Python 2)
 python3-dolfin - Python interface for DOLFIN (Python 3)
Changes:
 dolfin (2017.2.0.post0-2) unstable; urgency=medium
 .
   * debian/control: update VCS tags to salsa.debian.org
Checksums-Sha1:
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Accepted ufl 2017.2.0.0-2 (source) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 21 Feb 2018 22:34:08 +0800
Source: ufl
Binary: python-ufl python3-ufl python-ufl-doc
Architecture: source
Version: 2017.2.0.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Team 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 python-ufl - unified language for form-compilers (Python 2)
 python-ufl-doc - documentation and demos for UFL
 python3-ufl - unified language for form-compilers (Python 3)
Changes:
 ufl (2017.2.0.0-2) unstable; urgency=medium
 .
   * debian/control: update VCS tags to salsa.debian.org
Checksums-Sha1:
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Accepted instant 2017.2.0.0-2 (source) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 21 Feb 2018 22:27:21 +0800
Source: instant
Binary: python-instant python3-instant
Architecture: source
Version: 2017.2.0.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Team 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 python-instant - simple inlining of C/C++ code in Python 2
 python3-instant - simple inlining of C/C++ code in Python 3
Changes:
 instant (2017.2.0.0-2) unstable; urgency=medium
 .
   * debian/control: update VCS tags to salsa.debian.org
Checksums-Sha1:
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Accepted fiat 2017.2.0.0-2 (source) into unstable

[Drew Parsons]

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Format: 1.8
Date: Wed, 21 Feb 2018 22:20:33 +0800
Source: fiat
Binary: python-fiat python3-fiat
Architecture: source
Version: 2017.2.0.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Team 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 python-fiat - tabulation of finite element function spaces (Python 2)
 python3-fiat - tabulation of finite element function spaces (Python 3)
Changes:
 fiat (2017.2.0.0-2) unstable; urgency=medium
 .
   * debian/control: Update VCS tags to salsa.debian.org
Checksums-Sha1:
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Accepted ffc 2017.2.0.post0-2 (source) into unstable

[Drew Parsons]

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Format: 1.8
Date: Wed, 21 Feb 2018 22:58:00 +0800
Source: ffc
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Architecture: source
Version: 2017.2.0.post0-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Team 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 python-ffc - compiler for finite element variational forms (Python 2)
 python3-ffc - compiler for finite element variational forms (Python 3)
Changes:
 ffc (2017.2.0.post0-2) unstable; urgency=medium
 .
   * Update VCS-git tag to https://salsa.debian.org
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Accepted dijitso 2017.2.0.0-2 (source) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 21 Feb 2018 22:43:50 +0800
Source: dijitso
Binary: python-dijitso python3-dijitso
Architecture: source
Version: 2017.2.0.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Team 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 python-dijitso - distributed just-in-time building of shared libraries (Python 
2)
 python3-dijitso - distributed just-in-time building of shared libraries 
(Python 3)
Changes:
 dijitso (2017.2.0.0-2) unstable; urgency=medium
 .
   * debian/control: update VCS tags to salsa.debian.org
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Accepted dolfin 2017.2.0.post0-1exp2 (source all amd64) into experimental, experimental

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Fri, 16 Feb 2018 15:34:44 +0800
Source: dolfin
Binary: libdolfin-dev libdolfin2017.2 python-dolfin python3-dolfin dolfin-doc 
dolfin-bin
Architecture: source all amd64
Version: 2017.2.0.post0-1exp2
Distribution: experimental
Urgency: medium
Maintainer: Debian Science Team 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 dolfin-bin - Executable scripts for DOLFIN
 dolfin-doc - Documentation and demo programs for DOLFIN
 libdolfin-dev - Shared links and header files for DOLFIN
 libdolfin2017.2 - Shared libraries for DOLFIN
 python-dolfin - Python interface for DOLFIN (Python 2)
 python3-dolfin - Python interface for DOLFIN (Python 3)
Changes:
 dolfin (2017.2.0.post0-1exp2) experimental; urgency=medium
 .
   * reorganise debian/copyright: collect core DOLFIN files and
 contributors in one entry.
   * Remove -dbg packages from debian/control.
 Debug packages (-dbgsym) are built automatically.
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Re: dolfin_2017.2.0.post0-1exp1_amd64.changes REJECTED

[Drew Parsons]

On Wed, 2018-02-14 at 11:04 +0800, Drew Parsons wrote:
> On Wed, 2018-02-14 at 10:47 +0800, Drew Parsons wrote:
> > On Tue, 2018-02-13 at 22:00 +, Thorsten Alteholz wrote:
> > > Hi Drew,
> > > 
> > > one of our trainees had a look at your package and found:
> > >  * copyright file, while autogenerated and unreadable,
> > > incomplete.
> > > missing for example:
> > > test/unit/cpp/mesh/MeshColoring.cpp:// Copyright (C) 2016
> > > Garth
> > > N. Wells
> > 
> > Thanks, should be easy to fix.
> > 
> 
> Actually, looking more closely, that objection does not make
> sense.  That file and Garth Wells are already listed under the main
> copyright entry:
> 
> Files: *
> Copyright: 2002-2015, Anders Logg, Garth N. Wells, et al
> License: LGPL-3+
> 
> Can you please review the review?
> 

I'm guessing this is the problem: that explicit test/unit/mesh/ entries
are listed for Anders Logg (Mesh.cpp, MeshValueCollection.cpp), but not
for Garth N. Wells (MeshFunction.cpp is listed but MeshColoring.cpp is
not).

What I can do is reorganise copyright so there is only one single 
LGPL-3+ entry with Files: * (at least for all LGPL-3+ files marked
"This file is part of DOLFIN"),  with a collective year 2002-2017 and
listing all of the individual contributors together in the one place.

Drew



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Re: dolfin_2017.2.0.post0-1exp1_amd64.changes REJECTED

[Drew Parsons]

On Wed, 2018-02-14 at 10:47 +0800, Drew Parsons wrote:
> On Tue, 2018-02-13 at 22:00 +, Thorsten Alteholz wrote:
> > Hi Drew,
> > 
> > one of our trainees had a look at your package and found:
> >  * copyright file, while autogenerated and unreadable, incomplete.
> > missing for example:
> > test/unit/cpp/mesh/MeshColoring.cpp:// Copyright (C) 2016 Garth
> > N. Wells
> 
> Thanks, should be easy to fix.
> 
Actually, looking more closely, that objection does not make
sense.  That file and Garth Wells are already listed under the main
copyright entry:

Files: *
Copyright: 2002-2015, Anders Logg, Garth N. Wells, et al
License: LGPL-3+

Can you please review the review?


> > Is there a reason why you manually added a debu package?
> 
> Probably not.  

More detail: I think it comes historically.  Automatic generation of
debug packages is relatively new.  Before then we had to add them
manually. I can remove the explicit entries now.

Drew

> 
> Can you process petsc?
> 
> Thanks,
> Drew
> 
> 
> > Thanks!
> >  Thorsten
> > 
> > 
> > 
> > ===
> > 
> > Please feel free to respond to this email if you don't understand
> > why
> > your files were rejected, or if you upload new files which address
> > our
> > concerns.

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Re: dolfin_2017.2.0.post0-1exp1_amd64.changes REJECTED

[Drew Parsons]

On Tue, 2018-02-13 at 22:00 +, Thorsten Alteholz wrote:
> Hi Drew,
> 
> one of our trainees had a look at your package and found:
>  * copyright file, while autogenerated and unreadable, incomplete.
> missing for example:
> test/unit/cpp/mesh/MeshColoring.cpp:// Copyright (C) 2016 Garth
> N. Wells

Thanks, should be easy to fix.

> Is there a reason why you manually added a debu package?

Probably not.  

Can you process petsc?

Thanks,
Drew


> Thanks!
>  Thorsten
> 
> 
> 
> ===
> 
> Please feel free to respond to this email if you don't understand why
> your files were rejected, or if you upload new files which address
> our
> concerns.
> 

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Accepted superlu-dist 5.3.0+dfsg1-1 (source amd64) into unstable

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sat, 10 Feb 2018 12:25:13 +0800
Source: superlu-dist
Binary: libsuperlu-dist-dev libsuperlu-dist5
Architecture: source amd64
Version: 5.3.0+dfsg1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 libsuperlu-dist-dev - Highly distributed solution of sparse linear equations
 libsuperlu-dist5 - Highly distributed solution of sparse linear equations
Changes:
 superlu-dist (5.3.0+dfsg1-1) unstable; urgency=medium
 .
   * New upstream version.
   * debian patch mc64ad_dist-stub.patch: Identify SuperLU-Dist in
 "mc64 unsupported" error message.
   * Standards-Version: 4.1.3
   * debhelper compatibility level 11
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superlu-dist_5.3.0+dfsg1-1_amd64.buildinfo

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Accepted ffc 2017.2.0.post0-1exp1 (source all) into experimental

[Drew Parsons]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 07 Feb 2018 00:23:32 +0800
Source: ffc
Binary: python-ffc python3-ffc
Architecture: source all
Version: 2017.2.0.post0-1exp1
Distribution: experimental
Urgency: medium
Maintainer: Debian Science Team 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
 python-ffc - compiler for finite element variational forms (Python 2)
 python3-ffc - compiler for finite element variational forms (Python 3)
Changes:
 ffc (2017.2.0.post0-1exp1) experimental; urgency=medium
 .
   * New upstream release.
 - this is the official 2017.2.0 release.
   The previous version was a mislabelled beta release.
   * Standards-Version: 4.1.3
   * debhelper compatibility level 11
   * Priority: optional not extra
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Bug#886715: sasview-doc: unified_power_Rg docs point at _rg not _Rg

[Drew Parsons]

Package: sasview-doc
Version: 4.2.0~git20171031-3
Severity: normal

When clicking on the Help button for the unified_power_Rg model (Shape
Independent), sasview looks for unified_power_rg.html (more precisely
/usr/lib/python2.7/dist-packages/sas/sasview/doc/user/models/unified_power_rg.html
 )

But the doc file is unified_power_Rg.html (i.e. _Rg not _rg), so the
help page is not found.

All the other html files in that doc dir are lowercase, so the bug
probably only applies to unified_power_Rg.

-- System Information:
Debian Release: buster/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.14.0-3-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), 
LANGUAGE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages sasview-doc depends on:
ii  libjs-jquery 3.2.1-1
ii  libjs-mathjax2.7.2+dfsg-1
ii  libjs-sphinxdoc  1.6.5-4

sasview-doc recommends no packages.

sasview-doc suggests no packages.

-- no debconf information

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Bug#860599: libmpich-dev: provide alternative mpi-fort.pc

[Drew Parsons]

affects 860599 - mumps
thanks

On Wed, 19 Apr 2017 12:22:37 +0800 Drew Parsons <dpars...@debian.org>
wrote:
> 
> The mpi alternatives provide several pkg-config files: mpi-c.pc,
> mpi-cxx.pc, mpi-fort.pc, mpi.pc, all provided by openmpi.
> 
> But mpich only provides mpi.pc
> 
> This somewhat breaks usage of mpi-defaults, since it means we can't
> rely on these alternatives existing.  For instance, MUMPS FTBFS on
> m68k because mpi-fort is not available.
> 

As far as mumps goes, it now (5.1.2-4) builds using mpicc/mpifort which
mitigates the need for mpi-fort.pc (mpifort is constructed to add the
required MPI libraries).  So mumps is no longer directly affected.  

Still makes sense to provide consistent pkg-config files though, I
think.

Drew

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Re: sasview_4.2.0~git20171031-1_amd64.changes REJECTED

[Drew Parsons]

On Sat, 2017-12-23 at 19:00 +, Thorsten Alteholz wrote:
> Hi Drew,
> 
> I am sorry, but as CC-Attribution-ShareAlike is not yet listed 
> in /usr/share/common-licenses/ the full text should be in your 
> debian/copyright.

It's bloody long...

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Bug#884939: mumps: FTBFS on m68k: mpi-fort.pc not found, mpi_* undefined

[Drew Parsons]

affects 860599 mumps
thanks


On Thu, 21 Dec 2017 14:00:36 -0500 "Aaron M. Ucko" 
wrote:
> Source: mumps
> Version: 5.1.1-3+b1
> Severity: important
> Tags: upstream
> Justification: fails to build from source
> User: debian-...@lists.debian.org
> Usertags: m68k
> 
> Builds of mumps for m68k (admittedly not a release architecture) have
> been failing as detailed in [1]:
> 
>   Package mpi-fort was not found in the pkg-config search path.
>   Perhaps you should add the directory containing `mpi-fort.pc'


Thanks Aaron, I'm aware of the problem, in fact it's Bug#860599. 
OpenMPI provides mpi-fort.pc and mumps is tuned to use it. 
Unfortunately mpich doesn't provide it, and mpich is the default MPI on
m68k (notice also that sh4 has the same problem).

Rather than merging this bug into #860599, I'll keep them separate in
case people want to discuss or make a patch for mumps to not require
mpi-fort.pc.

But I think a tidier solution is to construct an mpi-fort.pc for mpich.
  (or perhaps as you suggest, using mpifort itself is the better
solution)

Drew

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Re: sasview_4.1.2-1_amd64.changes REJECTED

[Drew Parsons]

Thanks Thorsten. Fixed in sasview 4.2.0~git20171031-1.

Drew

On Thu, 2017-12-21 at 19:00 +, Thorsten Alteholz wrote:
> Hi Drew,
> 
> please mention 
>  sasview-4.1.2/src/sas/sasgui/guiframe/images/report.png
> in your debian/copyright.
> 
> While you are at it, please also take care of all those:
> 
> E: sasview-doc: privacy-breach-uses-embedded-file
> usr/share/doc/sasview-doc/html/dev/api/modules.html You may use the
> libjs-mathjax package. (https://cdnjs.cloudflare.com/ajax/libs/mat
> hjax/2.7.1/mathjax.js?config=tex-mml-am_chtml)
> E: sasview-doc: privacy-breach-uses-embedded-file
> usr/share/doc/sasview-doc/html/dev/api/src.html You may use the
> libjs-mathjax package. (https://cdnjs.cloudflare.com/ajax/libs/mathja
> x
> /2.7.1/mathjax.js?config=tex-mml-am_chtml)
> E: sasview-doc: privacy-breach-uses-embedded-file
> usr/share/doc/sasview-doc/html/dev/api/src.sas.html You may use the
> libjs-mathjax package. (https://cdnjs.cloudflare.com/ajax/libs/mat
> hjax/2.7.1/mathjax.js?config=tex-mml-am_chtml)
> E: sasview-doc: privacy-breach-uses-embedded-file
> usr/share/doc/sasview-
> doc/html/dev/api/src.sas.sascalc.calculator.c_extensions.html You may
> use the libjs-mathjax package. (https://cd
> njs.cloudflare.com/ajax/libs/mathjax/2.7.1/mathjax.js?config=tex-mml-
> am_chtml)
> (...)
> 
> Thanks!
>  Thorsten
> 
> 
> 
> ===
> 
> Please feel free to respond to this email if you don't understand why
> your files were rejected, or if you upload new files which address
> our
> concerns.
> 

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Bug#884121: Build-Depends: libhypre-dev, but does not build against HYPRE

[Drew Parsons]

Package: freefem++
Version: 3.47+dfsg1-2
Severity: normal

freefem++ Build-Depends: libhypre-dev, and checks for hypre during
configure. 

But in the rest of the build HYPRE is not actually used.  There are
files that include hypre headers in src/solver and in examples++-mpi, but the
examples build doesn't invoke the hypre files.  src/solver isn't being used at 
all.

I'm not sure if it means the configure or Makefile.am settings should be
patched, or if Build-Depends: libhypre-dev should just be removed.


-- System Information:
Debian Release: buster/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.14.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), 
LANGUAGE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages freefem++ depends on:
ii  freeglut32.8.1-3
ii  libarpack2   3.5.0+real-1
ii  libatlas3-base [libblas.so.3]3.10.3-5
ii  libblas3 [libblas.so.3]  3.7.1-4
ii  libc62.25-3
ii  libgcc1  1:7.2.0-17
ii  libgl1   1.0.0-1
ii  libglu1-mesa [libglu1]   9.0.0-2.1
ii  libhdf5-100  1.10.0-patch1+docs-4
ii  libopenblas-base [libblas.so.3]  0.2.20+ds-4
ii  libopenmpi2  2.1.1-7
ii  libstdc++6   7.2.0-17
ii  libumfpack5  1:4.5.6-1

freefem++ recommends no packages.

freefem++ suggests no packages.

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Bug#883842: superlu: Source includes "SRC/mc64ad.c" listed in Files-Excluded header

[Drew Parsons]

On Fri, 08 Dec 2017 09:58:34 + Chris Lamb  wrote:
> 
> So, I would add an override for the "source-includes-file-in-files-
excluded"
> Lintian tag and include an explanation there. That should cover it I
think.
> 

I think that's a bug in lintian, if it's judging source files on the
contents after applying debian patches.

Drew

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Bug#700087: libmumps-dev: Please package the Scilab module

[Drew Parsons]

Hi Sylvestre,

both scilab and mumps are recently updated (latest versions in
experimental).

Are you still able to work on the scilab module for mumps?

Drew

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Re: Comments regarding slepc_3.8.1+dfsg1-1_amd64.changes

[Drew Parsons]

On Sun, 2017-11-26 at 15:36 +, Thorsten Alteholz wrote:
> Hi Drew,
> 
> I marked your package for accept, but there are some issues found by
> one of our trainees:
>  * all html files include , which
> is reported by lintian
>  * html files for sources are not regenerated
>  * a lot of autogenerated interface files for c-to-fortran, not
> rebuilt
> 
> Please take care of them in a later upload.
> 
> Thanks!
>  Thorsten
> 
> 


Thanks Thorsten!  I'll try to sort out those issues before we next need
to update via the NEW queue.

Drew



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Bug#882667: hypre: CUDA support: hacks impeded by -W flags

[Drew Parsons]

On Sat, 25 Nov 2017 20:24:50 +0800 Drew Parsons <dpars...@debian.org>
wrote:
> 
> Again, the problem is that -W is not recognised by nvcc.  Would have
> to hack the soname patch to encapsulate it inside --compiler-options

Can get further using nvcc --linker-options to carry -Wl options.

But "CC=mpiCC CUDACXX=mpiCC dh_auto_configure" seems better than
"CC=nvcc", together with export OMPI_CXX=g++-5 to set mpiCC.

With other sundry hacks, gets to src/struct_mv and stalls at
assumed_part.c, apparently because of inconsistencies in C/C++
standards between nvcc and CC.Depending on whether g++-5 or clang++-3.8 
is used, whether -std=c++11 or c++14 or c++98 is passed to gcc, get
either

 - conflict in multiple definitions of isnan, conflicting between 
CUDA's /usr/include/math_functions.h and /usr/include/x86_64-linux-
gnu/bits/mathcalls.h

 - or similar multiple definitions in abs(float)

 - or  /usr/include/cuda_fp16.h:985:68: error: C does not support default 
arguments
__CUDA_FP16_DECL__ __half2 __shfl(__half2 var, int delta, int width=warpSize);

- or inconsistent C/C++ definitions
./_hypre_struct_mv.h:1464:8: error: expected identifier or '('
extern "C++" {
   ^
./_hypre_struct_mv.h:1488:22: error: unexpected OpenMP directive '#pragma 
omp parallel for'
#pragma omp parallel for schedule(static)

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Bug#882667: hypre: CUDA support: hacks impeded by -W flags

[Drew Parsons]

Source: hypre
Version: 2.13.0-1exp1
Severity: normal

With some hacking, we can start attempting to build hypre with CUDA
support (private build, or perhaps a separate hypre package in contrib).

Brief notes:

- The version of nvcc (nvidia-cuda-toolkit) in debian non-free is 8.0.61-3
nvcc does not yet support gcc 7, and nvcc 8 does not support gcc 6
To also use mpiCC (so mpi.h is known, etc), need OMPI_CXX
So need 
  CC=nvcc CUDACXX=mpiCC dh_auto_configure -- $(extra_flags) --enable-shared

- nvcc does not recognise dpkg-buildflags flags (-W flags in
particular), so need to set an empty LDFLAGS and friends

- must hack src/config/configure.in where nvcc flags are defined,
replace -fPIC with --compiler-options '-fPIC'

- build with g++-5  fails at src/utilities/gpuMem.c:
$nvcc -O --compiler-options '-fPIC' -DUSE_NVTX -DHYPRE_USE_GPU 
-DHYPRE_USE_MANAGED  -ccbin=mpiCC -expt-extended-lambda -arch compute_35 
--std=c++11 -Xcompiler -fopenmp -Xcompiler   -DHYPRE_USE_CUDA  -DUSE_NVTX 
-DHYPRE_USE_GPU  -DHYPRE_USE_MANAGED -I /usr/local/cuda/include  
-DHAVE_CONFIG_H -I.. -I./.. -I.-c gpuMem.c
  gpuMem.c: In function ‘getstreamOlde’:
  gpuMem.c:335:23: error: storage size of ‘s’ isn’t constant
 static cudaStream_t s[MAXSTREAMS];
 ^
  gpuMem.c: In function ‘getdomain’:
  gpuMem.c:351:31: error: storage size of ‘h’ isn’t constant
   static nvtxDomainHandle_t h[MAXDOMAINS];
 ^
  gpuMem.c: In function ‘getevent’:
  gpuMem.c:364:22: error: storage size of ‘s’ isn’t constant
 static cudaEvent_t s[MAXEVENTS];


This gpuMem.c does compile cleanly under OMPI_CXX=clang++-3.8
Pass through using export OMPI_CXX=clang++-3.8 in debian/rules.

Finally then, using 
  export OMPI_CXX=clang++-3.8
  CC=nvcc CUDACXX=mpiCC dh_auto_configure -- $(extra_flags) --with-cuda 
--enable-unified-memory --with-nvcc --enable-shared

the libHYPRE_utilities.so build proceeds but fails at link time
providing the soname, 
  nvcc -shared -o libHYPRE_utilities-2.13.0.so amg_linklist.o binsearch.o 
exchange_data.o fortran_matrix.o hypre_ap.o hypre_complex.o hypre_memory.o 
hypre_printf.o hypre_qsort.o memory_dmalloc.o mpistubs.o qsplit.o random.o 
threading.o timer.o timing.o umalloc_local.o hypre_mpi_comm_f2c.o hypre_error.o 
F90_HYPRE_error.o hypre_prefix_sum.o hypre_merge_sort.o hypre_hopscotch_hash.o 
gpuErrorCheck.o gpuMem.o -lmpi -lm -Wl,-soname,libHYPRE_utilities-2.13.0.so 
-Wl,-z,defs
  nvcc fatal   : Unknown option 'Wl,-soname,libHYPRE_utilities-2.13.0.so'

Again, the problem is that -W is not recognised by nvcc.  Would have
to hack the soname patch to encapsulate it inside --compiler-options

Is it worth it?




-- System Information:
Debian Release: buster/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.13.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), 
LANGUAGE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
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Bug#865671: scotch hides build failures

[Drew Parsons]

tags 865671 moreinfo
thanks

On Fri, 23 Jun 2017 18:07:46 +0200 Helmut Grohne 
wrote:
> Source: scotch
> Version: 5.1.12b.dfsg-2
> 
> When some part of scotch's build fails (e.g. mpicc), the build
continues
> and may produce a broken package. This violates Debian Policy section
> 4.6. The cause is the use of an embedded makefile script without the
> recommended "set -e".
> 

This bug report is unconstructive.

Which makefile?

Which build failure?

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Bug#877054: #877054: hypre FTBFS with multiarch blas

[Drew Parsons]

Waiting for 2.11.2-1 to get through the NEW queue.

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Bug#876890: scalapack FTBFS on arm64: test failures

[Drew Parsons]

On Thu, 28 Sep 2017 15:28:11 +0800 Drew Parsons <dpars...@debian.org>
wrote:
> 
> The actual FTBFS is from the openmpi test:
> 
> OpenMPI tests failed:
>20 - dpb2tim (Failed)
> 

A test build on the porterbox succeeded.  The failure in your test must
have been a transitory openmpi problem.  

Please file scalapack for another test on arm64.

Drew

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Bug#876890: scalapack FTBFS on arm64: test failures

[Drew Parsons]

On Tue, 26 Sep 2017 21:09:03 +0300 Adrian Bunk  wrote:
> Source: scalapack
> Version: 2.0.2-3
> Severity: serious
> 
> Some recent change in unstable makes scalapack FTBFS on arm64:
> 
> https://tests.reproducible-builds.org/debian/history/scalapack.html
> https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/sc
alapack.html
> 
> ...
> The following tests FAILED:
> 1 - xCbtest (Failed)
> 2 - xFbtest (Failed)
>75 - xssvd (Failed)
>76 - xdsvd (Failed)
...

These are the mpich test failures, which are common and therefore
ignored.

The actual FTBFS is from the openmpi test:

OpenMPI tests failed:
 20 - dpb2tim (Failed)

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Bug#874712: python-h5py: all arches FTBFS

[Drew Parsons]

Package: python-h5py
Version: 2.7.0-1+b1
Severity: serious
Justification: FTBFS

Your new version of h5py fails to build from source.  All arches.

-- System Information:
Debian Release: buster/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.12.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), 
LANGUAGE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages python-h5py depends on:
ii  libc6 2.24-17
ii  libhdf5-100   1.10.0-patch1+docs-4
ii  python2.7.13-2
ii  python-numpy [python-numpy-abi9]  1:1.13.1-1
ii  python-six1.10.0-4

python-h5py recommends no packages.

Versions of packages python-h5py suggests:
ii  python-h5py-doc  2.7.0-1

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Re: dolfin_2017.1.0-1_amd64.changes REJECTED

[Drew Parsons]

On Sun, 2017-08-27 at 12:00 +, Luca Falavigna wrote:
> Hi,
> 
> libdolfin2017.1 gained a dependency on libparmetis4.0, which is in
> non-free.

Weird. parmetis support is explicitly switched off at configure time.  

Drew


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Bug#872911: mpi-default-dev: m68k not listed in OPENMPI_AVAILABLE_ARCHITECTURES

[Drew Parsons]

Package: mpi-default-dev
Version: 1.8
Severity: normal

OPENMPI_AVAILABLE_ARCHITECTURES in
/usr/share/mpi-default-dev/debian_defaults does not include m68k.

But openmpi is built on m68k (since 2.1.1-1), so it should now be added.

Similarly, powerpcspe is not listed in
MPICH_AVAILABLE_ARCHITECTURES.  That's consistent for the moment 
(mpich 3.3~a2-2 does not currently build on powerpcspe), but it did
build until recently (3.2-7+b1 was successful). From the logs the build
failure seems to be related to the gcc7 transition.

-- System Information:
Debian Release: buster/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.12.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), 
LANGUAGE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages mpi-default-dev depends on:
ii  libopenmpi-dev  2.1.1-6

mpi-default-dev recommends no packages.

mpi-default-dev suggests no packages.

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Bug#871279: libdolfin2016.2: requires rebuild against GCC 7 and symbols/shlibs bump

[Drew Parsons]

On Mon, 2017-08-07 at 17:44 +, Mattia Rizzolo wrote:
> 
> > dolfin 2017.1 is in the NEW queue, so that upgrade will handle this
> > bug.
> 
> Is the binary you uploaded built with gcc-7?  Otherwise that would
> not fix this bug.

It's been sitting in NEW for a month, so it would have been gcc-6 I
think.  But the upload is to experimental.  I figure we can ignore
anything in experimental, the symbols will get reset for the new ABI
when we drop it into unstable.

Drew

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Bug#871279: libdolfin2016.2: requires rebuild against GCC 7 and symbols/shlibs bump

[Drew Parsons]

On Mon, 07 Aug 2017 15:47:15 +0100 jcowg...@debian.org wrote:
> Package: libdolfin2016.2
> Version: 2016.2.0-5
> 
> It appears that your package provides an external symbol that is
> affected by the recent name mangling changes in GCC 7. See:
> https://gcc.gnu.org/gcc-7/porting_to.html#conversion-op-mangling
> 
...
> 
> - If your package is about to be renamed due to an upstream SONAME
bump,
>   you do not need to add any special symbols handling.
> 


dolfin 2017.1 is in the NEW queue, so that upgrade will handle this
bug.

Drew

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Bug#870054: freefem++: scalapack and blacs not found at build time

[Drew Parsons]

Source: freefem++
Version: 3.47+dfsg1-1
Severity: normal

blacs is about to be removed from the Debian archives, replaced by
scalapack2.0 (now in experimental).  So the configuration for the
freefem++ build will need to be updated to match. configure will need
to point the blacs library at -lscalapack$ff_with_mpi instead of
-lblacsCinit$ff_with_mpi, etc.

Actually there's another problem. Inspecting the current build logs,
neither blacs nor scalapack (the old versions currently still in
unstable) are currently being found at build time.  The logs (amd64)
report:
checking check hypre... yes
checking check superlu_dist... no
checking check superlu... yes
checking check superlu4... no
checking check blacs... no
checking check scalapack... no
checking check scotch... no
checking check ptscotch... no
checking check metis... no
checking check metis... yes
checking check parmetis... no

That should be fixed first, then it will be more clear how to
reconfigure for blacs in scalapack2.0.

Cheers,
Drew


-- System Information:
Debian Release: buster/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.11.0-2-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), 
LANGUAGE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

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Bug#863291: libscalapack-openmpi1: memory leak in pXgemr2d

[Drew Parsons]

On Tue, 25 Jul 2017 23:03:23 +0800 Drew Parsons <dpars...@debian.org>
wrote:
> Hi Grigory,
> 
> scalapack 2.0 is now available in experimental.
> 
> Could you test if your pXgemr2d problem persists when built against
> scalapack 2.0 with openmpi 2.1.1 ?

Note that scalapack 2.0 incorporates blacs, so your compile line would
be

mpif90 -O2 -o mx_pdgemr2d mx_pdgemr2d.f90  -llapack -lblas 
/usr/lib/x86_64-linux-gnu/libscalapack-openmpi.so.2.0

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Bug#863291: libscalapack-openmpi1: memory leak in pXgemr2d

[Drew Parsons]

Hi Grigory,

scalapack 2.0 is now available in experimental.

Could you test if your pXgemr2d problem persists when built against
scalapack 2.0 with openmpi 2.1.1 ?

Thanks,

Drew

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Bug#854228: Libraries not linked with their deps

[Drew Parsons]

On Tue, 21 Mar 2017 11:03:07 +0800 Drew Parsons <dpars...@debian.org>
wrote:
> On Tue, 21 Mar 2017 10:50:29 +0800 Drew Parsons <dpars...@debian.org>
> wrote:
> > 
> > That document is from 1997 though.  The MPI standard has moved
> through
> > 2 major versions since then. But blacs remains unchanged.
> 
> Further, BLACS is now part of (packaged with) scalapack, see
> http://netlib.org/scalapack/scalapack-2.0.0.html#_7_3_blacs_revamping
> 
> Probably the solution we want is to update our scalapack to 2.0.2,
and
> remove this blacs package, at least as a separate source package.


Confirming this is fixed in scalapack 2.0 (2.0.2-1exp3 is now in
experimental.

The initialisation code in BLACS/SRC/blacs_pinfo_.c now no longer
depends on whether Main is in F77 or not, i.e. the single 
libscalapack-openmpi.so library should be sufficient for use from both
C (via Cblacs_pinfo) or Fortran (via blacs_pinfo_).

Will close this bug when scalapack 2.0 transitions into unstable.

Drew

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Bug#868523: FTBFS: test failed 617 ML_MLP_NonSym_MPI_4, 668 Phalanx_dag_manager_MPI_1

[Drew Parsons]

On Mon, 17 Jul 2017 10:21:03 +0800 Drew Parsons <dpars...@debian.org>
wrote:
> 
> For whatever reason, the build does not fail on the buildd (odd, my
> test ran 842 tests, buildd only runs 830). 

Ah I see, you uploaded -4 while we were testing :)  
The bugserver didn't send me the bug traffic.

> Adding my build log again, the first attachment appears corrupted.

Still comes out corrupted in the gnome Archive Manager, but extracts
fine on the command line.

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Bug#865526: PETSc has strict dependency on MPI version

[Drew Parsons]

reopen 865526
retitle 865526 PETSc has strict dependency on MPI version
severity 865526 normal
forwarded 865526 
https://bitbucket.org/petsc/petsc/commits/ca70f86ee9db8e69523e0e69f12289c6cab9b4cb?at=jed/mpi-semver
thanks

Reopening to help track upstream handling of PETSc's MPI dependency
logic.

Until that's fixed, we need to lodge a binNMU for PETSc every time
openmpi (or mpich on m68k, sh4) is updated to a new upstream version.

Drew

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Bug#865526: libpetsc3.7.5-dev: uninstallable on current sid

[Drew Parsons]

On Fri, 30 Jun 2017 05:56:30 +0300 Adrian Bunk  wrote:
> 
> This is a release critical bug that should stay open until it is
fixed 
> in sid.


nmu has been filed in #866582 which will fix the bug in this instance.

The strict dependency of PETSc on the MPI version (that requires the
rebuild) is a bit of a nuisance.  It appears in
/usr/lib/petsc/include/petscsys.h.  In 3.7.6 they have a strict
equality on the OMPI version dependency.  I've contacted them about it
and they've made a patch to relax it to a minor version dependency
rather than a release (patch) version dependency, which
should help us.

That patch is held at
https://bitbucket.org/petsc/petsc/commits/ca70f86ee9db8e69523e0e69f1228
9c6cab9b4cb?at=jed/mpi-semver
but looks like it hasn't been merged to upstream master yet.  

We should talk to upstream about it again.

Drew

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Bug#863828: python3-instant: undefined symbol: PyClass_Type during interpolate

[Drew Parsons]

On Thu, 1 Jun 2017 10:39:37 +0200 Johannes Ring <joha...@simula.no>
wrote:
> On Thu, Jun 1, 2017 at 10:24 AM, Drew Parsons <dpars...@debian.org>
wrote:
> > Should the vtk section in UseDOLFIN.cmake be controlled with some
> > python3 test, so VTK is still pulled in for python2?
> 
> Yes, we can do that, although I believe the vtk section in
> UseDOLFIN.cmake is not important. I will make a patch.


It's still failing, with python-ffc 2016.2.0-3 and libdolfin-dev
2016.2.0-4 (with UseDOLFIN.cmake patched).

In [4]: u = interpolate(Expression('x[0] + x[1]', degree=1), V)
Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
--- Instant: compiling ---
In instant.import_module_directly: Failed to import module 
'dolfin_ee8f3791ac0429f005de8924557ccde25f2d90f2' from 
'/home/drew/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0429f005de8924557ccde25f2d90f2';
ImportError:dynamic module does not define module export function 
(PyInit__dolfin_ee8f3791ac0429fd87a23c24557ccde25f2d90f2);
Failed to import module found in cache. Modulename: 
'dolfin_ee8f3791ac0429fd87a23c24557ccde25f2d90f2';
Path: 
'/home/useruser/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0429fd87a23c24557ccde25f2d90f2';
ImportError:dynamic module does not define module export function 
(PyInit__dolfin_ee8f3791ac0429fd87a23c24557ccde25f2d90f2);
---
AssertionErrorTraceback (most recent call last)
 in ()
> 1 u = interpolate(Expression('x[0] + x[1]', degree=1), V)

/usr/lib/python3/dist-packages/dolfin/functions/expression.py in __new__(cls, 
cppcode, *args, **kwargs)
652 cpp_base, members = compile_expressions([cppcode],
653 
[generic_function_members],
--> 654 
mpi_comm=kwargs.get("mpi_comm"))
655 cpp_base, members = cpp_base[0], members[0]
656 

/usr/lib/python3/dist-packages/dolfin/compilemodules/expressions.py in 
compile_expressions(cppargs, generic_function_members, mpi_comm)
212 "\n\n".join(code_snippets), classnames,
213 additional_declarations="\n".join(additional_declarations),
--> 214 mpi_comm=mpi_comm)
215 
216 return expression_classes, all_members

/usr/lib/python3/dist-packages/dolfin/compilemodules/expressions.py in 
compile_expression_code(code, classnames, module_name, additional_declarations, 
mpi_comm)
139 compiled_module = compile_extension_module(
140 code, additional_declarations=additional_declarations,
--> 141 mpi_comm=mpi_comm)
142 
143 # Get the compiled class

/usr/lib/python3/dist-packages/dolfin/compilemodules/jit.py in mpi_jit(*args, 
**kwargs)
 66 # Just call JIT compiler when running in serial
 67 if MPI.size(mpi_comm) == 1:
---> 68 return local_jit(*args, **kwargs)
 69 
 70 # Compile first on process 0

/usr/lib/python3/dist-packages/dolfin/compilemodules/compilemodule.py in 
compile_extension_module(code, module_name, additional_declarations, 
additional_system_headers, mpi_comm, **instant_kwargs)
470 code=code,
471 additional_declarations=additional_declarations,
--> 472 **instant_kwargs)
473 
474 sys.stdout.flush()

/usr/lib/python3/dist-packages/instant/build.py in build_module(modulename, 
source_directory, code, init_code, additional_definitions, 
additional_declarations, sources, wrap_headers, local_headers, system_headers, 
include_dirs, library_dirs, libraries, swigargs, swig_include_dirs, cppargs, 
lddargs, object_files, arrays, generate_interface, generate_setup, 
cmake_packages, signature, cache_dir)
585 
586 # Import module and place in memory cache
--> 587 module = import_and_cache_module(module_path, modulename, 
moduleids)
588 
589 if not module:

/usr/lib/python3/dist-packages/instant/cache.py in 
import_and_cache_module(path, modulename, moduleids)
 90 module, e = import_module_directly(path, modulename)
 91 instant_assert(module is not None, "Failed to import module found 
in cache. Modulename: '%s';\nPath: '%s';\n%s:%s;" % (modulename, path, 
type(e).__name__,
---> 92 
   e))
 93 for moduleid in moduleids:
 94 place_module_in_memory_cache(moduleid, module)

/usr/lib/python3/dist-packages/instant/output.py in instant_assert(condition, 
*message)
101 _log.error(*message)
102 text = message[0] % message[1:]
--> 103 raise AssertionError(text)
104 
105 

AssertionError: Failed to import module found in cache. Modulename

Bug#863828: python3-instant: undefined symbol: PyClass_Type during interpolate

[Drew Parsons]

reassign 863828 libdolfin-dev 2016.2.0-3
thanks

On Thu, 2017-06-01 at 10:01 +0200, Johannes Ring wrote:
> 
> The problem here is that Python 2 header files are used. This comes
> from VTK, which is built against Python 2 only. The solution is to
> not
> call `find_package(VTK)` and `include(${VTK_USE_FILE})` in
> /usr/share/dolfin/cmake/UseDOLFIN.cmake. It can be verified that this
> fixes the problem by removing these lines in UseDOLFIN.cmake.
> 
> This is a bug in dolfin, not instant. Drew: could you re-target this
> to dolfin (perhaps libdolfin-dev)?

Reassigned.

Should the vtk section in UseDOLFIN.cmake be controlled with some
python3 test, so VTK is still pulled in for python2?

Drew

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Bug#863829: python2: dolfin 'module' object has no attribute 'cpp'

[Drew Parsons]

Package: python-dolfin
Version: 2016.2.0-3
Severity: grave
Justification: renders package unusable

Weird, the new python3 module seems to have broken the python2 dolfin
module.  That's not good.

Importing dolfin gives the error:
AttributeError: 'module' object has no attribute 'cpp'

Importing in python3 does not have this error.

$ ipython
Python 2.7.13 (default, Jan 19 2017, 14:48:08) 
In [1]: import dolfin
---
AttributeErrorTraceback (most recent call last)
 in ()
> 1 import dolfin

/usr/lib/python2.7/dist-packages/dolfin/__init__.pyc in ()
 15 
 16 # Import names from the compiled cpp modules
---> 17 from . import cpp
 18 from dolfin.cpp import *
 19 from dolfin.cpp import __version__, __swigversion__, __pythonversion__

/usr/lib/python2.7/dist-packages/dolfin/cpp/__init__.py in ()
 41 
 42 # Import the module
---> 43 exec("from . import %s" % module_name)
 44 module = globals()[module_name]
 45 

 in ()

/usr/lib/python2.7/dist-packages/dolfin/cpp/la.py in ()
233 make_ufc_form = _la.make_ufc_form
234 import dolfin.cpp.common
--> 235 class LinearAlgebraObject(dolfin.cpp.common.Variable):
236 """
237 

AttributeError: 'module' object has no attribute 'cpp'




-- System Information:
Debian Release: 9.0
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64
 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.9.0-3-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages python-dolfin depends on:
ii  libc6 2.24-11
ii  libdolfin-dev 2016.2.0-3
ii  libdolfin2016.2   2016.2.0-3
ii  libgcc1   1:6.3.0-18
ii  libgomp1  6.3.0-18
ii  libopenmpi2   2.0.2-2
ii  libpetsc3.7.5 [libpetsc3.7]   3.7.5+dfsg1-4+b1
ii  libpetsc3.7.6 [libpetsc3.7]   3.7.6+dfsg1-1exp1
ii  libpython2.7  2.7.13-2
ii  libslepc3.7.3 [libslepc3.7]   3.7.3+dfsg1-5
ii  libstdc++66.3.0-18
ii  python2.7.13-2
ii  python-dijitso2016.2.0-1
ii  python-ffc2016.2.0-2
ii  python-instant2016.2.0-2
ii  python-numpy [python-numpy-abi9]  1:1.12.1-3
ii  python-petsc4py   3.7.0-3
ii  python-ply3.9-1
ii  python-six1.10.0-4
ii  python-slepc4py   3.7.0-3
ii  python-sympy  1.0-3
ii  python-ufl2016.2.0-2
pn  python:any
ii  swig3.0   3.0.10-1.1

python-dolfin recommends no packages.

Versions of packages python-dolfin suggests:
ii  dolfin-doc  2016.2.0-3

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Bug#863828: python3-instant: undefined symbol: PyClass_Type during interpolate

[Drew Parsons]

Package: python3-instant
Version: 2016.2.0-2
Severity: normal

Testing the new python3 dolfin.  It works fine on my own scripts. But
seems to fail when instant is invoked by interpolate.

$ instant-clean-3 
$ ipython3
Python 3.5.3 (default, Jan 19 2017, 14:11:04) 
In [1]: from fenics import *  # dolfin module behaves the same
In [2]: mesh = UnitSquareMesh(2, 2)
In [3]: V = FunctionSpace(mesh, 'P', 1)
In [4]: u = interpolate(Expression('x[0] + x[1]', degree=1), V)
...
AssertionError: Failed to import module found in cache. Modulename: 
'dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2';
Path: 
'/home/user/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2';
ImportError:/home/user/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2/_dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2.so:
 undefined symbol: PyClass_Type;



The full error report is:

In [4]: u = interpolate(Expression('x[0] + x[1]', degree=1), V)
Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
--- Instant: compiling ---
In instant.import_module_directly: Failed to import module 
'dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2' from 
'/home/user/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2';
ImportError:/home/user/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2/_dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2.so:
 undefined symbol: PyClass_Type;
Failed to import module found in cache. Modulename: 
'dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2';
Path: 
'/home/user/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2';
ImportError:/home/user/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2/_dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2.so:
 undefined symbol: PyClass_Type;
---
AssertionErrorTraceback (most recent call last)
 in ()
> 1 u = interpolate(Expression('x[0] + x[1]', degree=1), V)

/usr/lib/python3/dist-packages/dolfin/functions/expression.py in __new__(cls, 
cppcode, *args, **kwargs)
652 cpp_base, members = compile_expressions([cppcode],
653 
[generic_function_members],
--> 654 
mpi_comm=kwargs.get("mpi_comm"))
655 cpp_base, members = cpp_base[0], members[0]
656 

/usr/lib/python3/dist-packages/dolfin/compilemodules/expressions.py in 
compile_expressions(cppargs, generic_function_members, mpi_comm)
212 "\n\n".join(code_snippets), classnames,
213 additional_declarations="\n".join(additional_declarations),
--> 214 mpi_comm=mpi_comm)
215 
216 return expression_classes, all_members

/usr/lib/python3/dist-packages/dolfin/compilemodules/expressions.py in 
compile_expression_code(code, classnames, module_name, additional_declarations, 
mpi_comm)
139 compiled_module = compile_extension_module(
140 code, additional_declarations=additional_declarations,
--> 141 mpi_comm=mpi_comm)
142 
143 # Get the compiled class

/usr/lib/python3/dist-packages/dolfin/compilemodules/jit.py in mpi_jit(*args, 
**kwargs)
 66 # Just call JIT compiler when running in serial
 67 if MPI.size(mpi_comm) == 1:
---> 68 return local_jit(*args, **kwargs)
 69 
 70 # Compile first on process 0

/usr/lib/python3/dist-packages/dolfin/compilemodules/compilemodule.py in 
compile_extension_module(code, module_name, additional_declarations, 
additional_system_headers, mpi_comm, **instant_kwargs)
470 code=code,
471 additional_declarations=additional_declarations,
--> 472 **instant_kwargs)
473 
474 sys.stdout.flush()

/usr/lib/python3/dist-packages/instant/build.py in build_module(modulename, 
source_directory, code, init_code, additional_definitions, 
additional_declarations, sources, wrap_headers, local_headers, system_headers, 
include_dirs, library_dirs, libraries, swigargs, swig_include_dirs, cppargs, 
lddargs, object_files, arrays, generate_interface, generate_setup, 
cmake_packages, signature, cache_dir)
585 
586 # Import module and place in memory cache
--> 587 module = import_and_cache_module(module_path, modulename, 
moduleids)
588 
589 if not module:

/usr/lib/python3/dist-packages/instant/cache.py in 
import_and_cache_module(path, modulename, moduleids)
 90 module, e = import_module_directly(path, modulename)
 91 instant_assert(module is not None, "Failed to import module found 
in cache. Modulename: '%s';\nPath: '%s';\n%s:%s;" % (modulename, path, 
type(e).__name__,
---> 92 
   e))
 93 

Bug#860599: libmpich-dev: provide alternative mpi-fort.pc

[Drew Parsons]

Package: libmpich-dev
Version: 3.2-7+b1
Severity: normal

The mpi alternatives provide several pkg-config files: mpi-c.pc,
mpi-cxx.pc, mpi-fort.pc, mpi.pc, all provided by openmpi.

But mpich only provides mpi.pc

This somewhat breaks usage of mpi-defaults, since it means we can't
rely on these alternatives existing.  For instance, MUMPS FTBFS on
m68k because mpi-fort is not available.

Should an mpich version of mpi-fort.pc (and mpi-c.pc, mpi-cxx.pc) be
created and added to the mpich alternatives?

-- System Information:
Debian Release: 9.0
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.9.0-2-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages libmpich-dev depends on:
ii  g++ 4:6.3.0-4
ii  gfortran4:6.3.0-4
ii  libc6   2.24-10
ii  libcr-dev   0.8.5-2.3+b1
ii  libcr0  0.8.5-2.3+b1
ii  libmpich12  3.2-7+b1

Versions of packages libmpich-dev recommends:
ii  mpich  3.2-7+b1

libmpich-dev suggests no packages.

-- no debconf information

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Bug#859492: mumps: Incomplete debian/copyright?

[Drew Parsons]

tags 859492 + fixed pending
thanks

On Tue, 2017-04-04 at 10:03 +0100, Chris Lamb wrote:
> 
> I just ACCEPTed mumps from NEW but noticed it was missing
> attribution 
> in debian/copyright for at least src/ana_orderings.F.
> 
> (This is not exhaustive so please check over the entire package 
> carefully and address these on your next upload.)
> 

Thanks Chris, I've added a copyright entry in git.

A copyright grep doesn't show up any other anomalies.

Drew

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Bug#822971: dolfin: FTBFS on kfreebsd

[Drew Parsons]

tags 822971 + fixed pending
thanks

A fix to build dolfin on kfreebsd is in git 2016.2.0-3, pending upload.

Drew

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Bug#826960: mumps: Please package with metis and parmetis

[Drew Parsons]

On Wed, 29 Mar 2017 17:13:13 +0800 Drew Parsons <dpars...@debian.org>
wrote:
>
> Hi Pierre, I'm preparing an update to mumps 5.1.  I'm following
> upstream's new debian template, which builds both scotch and metis at
> the same time.  This means libmumps-scotch-dev will have both scotch
> and metis support (similarly in the parallel version).  Is this
useful
> to you or would we be better to generate a strictly new separate
> package?
> 

Belay that.  metis has a non-free licence, so we can't build against it
without relegating mumps to contrib instead of the main archive.

It'll be easy for you to activate metis support yourself with a local
build.  For instance you could grab the experimental branch from the
debian git repo 
https://anonscm.debian.org/git/debian-science/packages/mumps.git
metis support was temporarily in place at commit
8d3d2aceffe4f90b35957cb98ace1c4370a69456

Drew

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Bug#826960: mumps: Please package with metis and parmetis

[Drew Parsons]

On Fri, 10 Jun 2016 18:36:52 +0200 (CEST) Pierre Saramito  wrote:
> Source: mumps
> Severity: wishlist
> 
> Dear Adam,
> 
> It would be nice to have libmumps-metis-dev and libmumps-parmetis-dev
> as alternatives to  and libmumps-ptscotch-dev
packages:
> please, could you package mumps with (par)metis also ?
> 

Hi Pierre, I'm preparing an update to mumps 5.1.  I'm following
upstream's new debian template, which builds both scotch and metis at
the same time.  This means libmumps-scotch-dev will have both scotch
and metis support (similarly in the parallel version).  Is this useful
to you or would we be better to generate a strictly new separate
package?

Drew

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Bug#858228: dolfin: PETSc and SCOTCH support disabled on kfreebsd

[Drew Parsons]

Source: dolfin
Version: 2016.2.0-3
Severity: normal

petsc and slepc are available on kfreebsd.  But dolfin configuration
is unable to activate their support due to a linking error during
configuration tests.  SCOTCH support also fails. A snippet from the
log gives:

  -- Checking for package 'PETSc'
  -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29") 
  -- Checking for one of the modules 'craypetsc_real;PETSc'
  -- Test PETSC_TEST_RUNS with shared library linking - Failed
  -- Test PETSC_TEST_RUNS static linking - Failed
  -- Check size of PetscInt
  -- Check size of PetscInt - done
  -- PETSc could not be found. Be sure to set PETSC_DIR. (missing:  
PETSC_TEST_RUNS) (found suitable version "3.7.5", minimum required is "3.6")
  -- Checking for package 'SCOTCH-PT'
  -- Found SCOTCH (version 5.1.1.12)
  -- Performing test SCOTCH_TEST_RUNS
  -- Performing test SCOTCH_TEST_RUNS - Failed
  -- Found ZLIB: /usr/lib/x86_64-kfreebsd-gnu/libz.so (found version "1.2.8") 
  -- Performing test SCOTCH_ZLIB_TEST_RUNS
  -- Performing test SCOTCH_ZLIB_TEST_RUNS - Failed
  -- SCOTCH could not be found. Be sure to set SCOTCH_DIR. (missing:  
SCOTCH_TEST_RUNS) 

I think the petsc error comes from /CMakeFiles/petsc_test_lib.cpp
It does successfully link manually, for instance with 
  gcc `pkg-config --cflags --libs PETSc mpi` petsc_test_lib.cpp
mpi is needed here due to the use of ompi_mpi_comm_self in
libpetsc_real.so.

Does dolfin's cmake/modules/FindPETSc.cmake need any adjustments in
order to successfully configure PETSc support on kfreebsd? 
(likewise FindSCOTCH.cmake ?)


-- System Information:
Debian Release: 9.0
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.9.0-2-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

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Bug#857692: petsc: FTBFS in !linux

[Drew Parsons]

On Thu, 16 Mar 2017 10:28:09 +0100 Mattia Rizzolo <mat...@debian.org>
wrote:
> On Thu, Mar 16, 2017 at 11:01:10AM +0800, Drew Parsons wrote:
> > The hurd failure looks like the common problem arising from the
changes
> > in PIE handling, see bugs #848129, #854061, same as the FTBFS on
other
> > tier 2 linux architectures.
> 
> Right, I asked for a give-back, and it seems like it's building fine
> now.
> 
> > The kfreebsd failure might need closer scrutiny.

Looks like kfreebsd is just another PIE victim. Seems to build now just
as well as it was before.  I've requested a give-back.

Drew

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Bug#857507: mesh generation module 'mshr' missing

[Drew Parsons]

On Fri, 17 Mar 2017 10:47:26 +0800 Drew Parsons <dpars...@debian.org>
wrote:
> 
> Hi Stephen

My apologies, your name is Steve not Stephen!

D.

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Bug#851183: fenics: Misses important 'mshr' module

[Drew Parsons]

On Fri, 13 Jan 2017 16:48:22 +0100 Hagen Fuchs  wrote:
> 
> > mshr needs a patched version of CGAL.
> 
> Ouf.  Anything I can do or is it simply a matter of just waiting for
the
> maintainers?
> 

Johannes has prepared a de-CGALed version in his  
johannr/optional-use-system-packages branch at
https://bitbucket.org/fenics-project/mshr/overview,
at commit 21d97cc, see
https://bitbucket.org/fenics-project/mshr/commits/all

If you're handy with git, it could be useful to test if it's working as
planned. Delete mshr's CGAL subdirectory and see if it correctly
locates the system CGAL.

mshr's CGAL copy also has some patches (that's part of the reason why
they kept their own copy) which we'll need to push to CGAL upstream.

Drew

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Bug#857507: mesh generation module 'mshr' missing

[Drew Parsons]

Package: python-dolfin
Version: 2016.2.0-2
Followup-For: Bug #857507

reassign 857507 fenics
forcemerge 851183 857507
thanks

Hi Stephen, mshr is another fenics component alongside dolfin. It's
not required for general dolfin usage, though of course your tutorial
example uses it.

The ftp-masters have blocked mshr from the archives since it uses a
local copy of CGAL, rather than the system CGAL, see
https://bugs.debian.org/824716
We're working with upsteam to enable a build with the system CGAL.

In the meantime the repo is
https://anonscm.debian.org/git/debian-science/packages/fenics/mshr.git/

Please build a local package from that.

Cheers,
Drew

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Bug#857692: petsc: FTBFS in !linux

[Drew Parsons]

On Tue, 14 Mar 2017 00:55:39 +0100 Mattia Rizzolo 
wrote:
> 
> petsc fails to build in hurd-i386, kfreebsd-i386 and kfreebsd-amd64.

The hurd failure looks like the common problem arising from the changes
in PIE handling, see bugs #848129, #854061, same as the FTBFS on other
tier 2 linux architectures.

The kfreebsd failure might need closer scrutiny.

Drew

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Bug#852514: libpetsc3.7-dev: leaves alternatives after purge: /usr/lib/petscdir/{3.7, 3.7-real}

[Drew Parsons]

> 
> 2m18.4s INFO: Warning: Package purging left files on system:
>   /etc/alternatives/petsc3.7 -> /usr/lib/petscdir/3.7.4/x86_64-linux-
gnu-real not owned
>   /etc/alternatives/petsc3.7-real -> /usr/lib/petscdir/3.7.4/x86_64-
linux-gnu-real   not owned
>   /usr/lib/petscdir/   owned by: libpetsc3.7.5-dev:amd64,
libpetsc3.7.4-dev:amd64
>   /usr/lib/petscdir/3.7 -> /etc/alternatives/petsc3.7  not
owned
>   /usr/lib/petscdir/3.7-real -> /etc/alternatives/petsc3.7-real   
 not owned



The petsc3.7 and petsc3.7-real alternative is set up by the
libpetsc3.7-dev.  At each installation (or upgrade) of libpetsc3.7-dev, 
the alternative is updated to the latest.

What's happening with this bug is that  3.7.4+dfsg1-9 is installed
first, setting up the 3.7.4 alternative. It's then upgraded to
3.7.5+dfsg1-3, setting up the 3.7.5 alternative.  But the 3.7.4
alternative remains in place.

When libpetsc3.7-dev is removed, prerm removes the petsc3.7
alternative. But the prerm script only deals with it's own version. So
only the 3.7.5 alternative is removed.  The 3.7.4 alternative remains
in place.

Then libpetsc3.7.Z-dev is removed, taking the alternative targets with
it. So when libpetsc3.7.4-dev is removed, the petsc3.7 alternative for
3.7.4 remains (see previous paragraph), but the 3.7.4 directories that
it points to no longer exists.

Looks like either libpetsc3.7.Z-dev should handle the petsc3.7
alternative instead of libpetsc3.7-dev.  Or they should at least test
for it on removal and clear the hanging links.

Drew

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Bug#852514: libpetsc3.7-dev: leaves alternatives after purge: /usr/lib/petscdir/{3.7, 3.7-real}

[Drew Parsons]

On Wed, 25 Jan 2017 02:42:20 +0100 Andreas Beckmann 
wrote:
> Package: libpetsc3.7-dev
> Version: 3.7.5+dfsg1-3
...
> 
> >From the attached log (scroll to the bottom...):
> 
> 2m18.4s INFO: Warning: Package purging left files on system:
>   /etc/alternatives/petsc3.7 -> /usr/lib/petscdir/3.7.4/x86_64-linux-
gnu-real not owned
>   /etc/alternatives/petsc3.7-real -> /usr/lib/petscdir/3.7.4/x86_64-
linux-gnu-real   not owned
>   /usr/lib/petscdir/   owned by: libpetsc3.7.5-dev:amd64,
libpetsc3.7.4-dev:amd64


Thanks Andreas. Looks like something went awry in libpetsc3.7.4-dev
3.7.4+dfsg1-9. I should be able to track it down.

Drew

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Bug#853029: mpi-default-dev: update mpi defaults for m68k and sh4 to openmpi?

[Drew Parsons]

On Mon, 2017-01-30 at 10:20 +0100, Mattia Rizzolo wrote:
> 
> Such change really needs to be ACK by a porter, therefore I'm CCing
> the
> 68k and sh lists.
> 

Thanks Mattia.  J.P. Adrian Glaubitz also replied via the port lists,
and said he'll check to confirm the change won't break anything.

Drew

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Bug#853029: mpi-default-dev: update mpi defaults for m68k and sh4 to openmpi?

[Drew Parsons]

Package: mpi-default-dev
Version: 1.8
Severity: normal

This bug report follows on from #833425
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=833425

openmpi now builds on m68k and sh4.

For various reasons it could be convenient if the Debian default
mpi on these architectures could be updated from mpich to openmpi.

The specific reason that bothers me is that mpich does not provide
mpi-fort.pc, while openmpi does.  This prevents mumps from building on
m68k and sh4 (with blacs-mpi also affected). 

Cheers,
Drew


-- System Information:
Debian Release: 9.0
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.9.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages mpi-default-dev depends on:
ii  libopenmpi-dev  2.0.2~git.20161225-9

mpi-default-dev recommends no packages.

mpi-default-dev suggests no packages.

-- no debconf information

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Bug#852011: petsc (libpetsc3.7.4-dev) depends on libgfortran-5-dev

[Drew Parsons]

On Fri, 20 Jan 2017 18:22:01 +0100 Matthias Klose 
wrote:
> 
> The severity of this report is likely to be raised before the
release,
> so that the gcc-5 package can be removed for the release.
> 


"Likely to be raised..." ??  The severity is already serious!

Drew

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Bug#802706: slepc: FTBFS: Unable to link with PETSc

[Drew Parsons]

On Thu, 2017-01-05 at 14:10 +0100, Santiago Vila wrote:
> found 802706 3.7.3+dfsg1-3
> thanks
> 
> Hi.
> 
> Sorry for the reopening but this is happening again in stretch.
> (I built this package 200 times, and it failed 200 times).
> 
> Build logs available here:
> 
> https://people.debian.org/~sanvila/build-logs/slepc/
> 
> Thanks.

It's not the same bug.  Attach the configure.log mentioned in the build
log.

It's hdf5 this time.

Drew

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Bug#847045: libtrilinos-zoltan-dev

[Drew Parsons]

On Mon, 5 Dec 2016 06:30:26 +0100 1...@gmx.us wrote:
> 
> Please compile PETSc with libtrilinos-zoltan-dev. At least
> as a recommended package. Like, libsuperlu-dev is now.
> 

trilinos has build pains at the moment.  We'll need that to settle out
first.

If we'll be supporting zoltan then probably makes sense to activate ml
support too.

Drew

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Re: Bug#846512: ITP: dijitso -- distributed just-in-time building of shared libraries

[Drew Parsons]

On Thu, 2016-12-08 at 14:43 +0100, Mattia Rizzolo wrote:
> On Thu, Dec 08, 2016 at 01:20:53AM +0800, Drew Parsons wrote:
> > 
> > looks like group members are locked out of the fenics subdir:
> > 
> > Can you provide group write access, chmod g+w /git/debian-
> > science/packages/fenics ?
> > 
> > Then I can add the new fenics/dijitsu repo.
> 
> Oh, yeah, of course!  done :)
> Sorry that bit was missing.


Thanks Mattia, looks like we're clear now.

Drew



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Bug#846512: ITP: dijitso -- distributed just-in-time building of shared libraries

[Drew Parsons]

Johannes Ring  wrote:
> 
> I have packaged dijitso locally but when I try to create a repository
> at https://anonscm.debian.org/git/debian-science/packages/fenics/diji
> tso.git
> I get a permission denied error. I am trying to use `gbp
> create-remote-repo`:
> 
> I guess I don't have permissions to create repositories. Can someone
> please help me create the repository?
> 


Hi Mattias,

looks like group members are locked out of the fenics subdir:

$ ls -ld /git/debian-science/packages/fenics
drwxr-sr-x+ 14 mattia debian-science 4096 Apr 23  2016 
/git/debian-science/packages/fenics

Can you provide group write access, chmod g+w 
/git/debian-science/packages/fenics ?

Then I can add the new fenics/dijitsu repo.

Cheers,
Drew

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Bug#802303: #802303: libpetsc3.6.2-dev: arch-dependent file in "Multi-Arch: same" package

[Drew Parsons]

I see what's going on a little better. The filepatch
/usr/share/python/runtime.d/libpetsc3.6.2-dev.rtupdate is common to all
arches, but its contents are architecture specific, which breaks Multi-
Arch:same.

Since that file was generated by dh_python2, it indicates that
dh_python2 is not [sufficiently] multiarch aware.  Perhaps related to
bug#798491.

But the actual python scripts themselves (.py in
/usr/lib/petscdir/3.7.4/x86_64-linux-gnu-real/bin) don't seem to be
architecture specific.  I wonder if it makes sense to split them off to
a common /usr/lib/petscdir/3.7.4/python dir.

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Bug#843010: elmerfem: hypre headers in /usr/include/hypre

[Drew Parsons]

Source: elmerfem
Version: 6.1.0.svn.5396.dfsg2-4
Severity: normal

hypre is now updated to 2.11.1.

The main impact that effects elmer is that the hypre header files have
been moved from the common directory to /usr/include/hypre.

Depending on how the elmer build scripts search for hypre, it's
possible they may need to be patched to look in the hypre subdir (if
they use something like "find /usr/include -name HYPRE.h" then no
patch would be needed).  Or there may be a place to add to CFLAGS
-I/usr/include/hypre.

Alternatively client files could be patched from
#include 
to
#include 

Cheers,
Drew



-- System Information:
Debian Release: stretch/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.7.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

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Bug#842405: paraview: can't load hdf5 file: vtkSISourceProxy: Failed to create vtkXdmfReader

[Drew Parsons]

Package: paraview
Version: 5.1.2+dfsg1-1+b1
Severity: normal

I'm trying to load a 1D HDF5 dataset (attached) into paraview, but it's crashing
with 

ERROR: In 
/build/paraview-MvSREd/paraview-5.1.2+dfsg1/ParaViewCore/ServerImplementation/Core/vtkSIProxy.cxx,
 line 310
vtkSISourceProxy (0x333fce0): Failed to create vtkXdmfReader. Aborting for 
debugging purposes.

Is this normal?

Reports on the web suggest this might happen when there is something
wrong with the build,
cf. http://public.kitware.com/pipermail/paraview/2016-March/036420.html



The backtrace is
(gdb) bt
#0  __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:58
#1  0x7401740a in __GI_abort () at abort.c:89
#2  0x72a2c35e in 
vtkSIProxy::CreateVTKObjects(paraview_protobuf::Message*) () from 
/usr/lib/paraview/libvtkPVServerImplementationCore.so.1
#3  0x72a41eb8 in 
vtkSISourceProxy::CreateVTKObjects(paraview_protobuf::Message*) () from 
/usr/lib/paraview/libvtkPVServerImplementationCore.so.1
#4  0x72a276ed in vtkSIProxy::Push(paraview_protobuf::Message*) () from 
/usr/lib/paraview/libvtkPVServerImplementationCore.so.1
#5  0x729ffe1a in 
vtkPVSessionCore::PushStateInternal(paraview_protobuf::Message*) () from 
/usr/lib/paraview/libvtkPVServerImplementationCore.so.1
#6  0x729fcd3f in 
vtkPVSessionCore::PushState(paraview_protobuf::Message*) () from 
/usr/lib/paraview/libvtkPVServerImplementationCore.so.1
#7  0x729fb655 in 
vtkPVSessionBase::PushState(paraview_protobuf::Message*) () from 
/usr/lib/paraview/libvtkPVServerImplementationCore.so.1
#8  0x766a0b96 in vtkSMProxy::CreateVTKObjects() () from 
/usr/lib/paraview/libvtkPVServerManagerCore.so.1
#9  0x766f3739 in vtkSMSourceProxy::CreateVTKObjects() () from 
/usr/lib/paraview/libvtkPVServerManagerCore.so.1
#10 0x766a0aef in vtkSMProxy::CreateVTKObjects() () from 
/usr/lib/paraview/libvtkPVServerManagerCore.so.1
#11 0x766f3739 in vtkSMSourceProxy::CreateVTKObjects() () from 
/usr/lib/paraview/libvtkPVServerManagerCore.so.1
#12 0x766a0460 in vtkSMProxy::UpdateVTKObjects() () from 
/usr/lib/paraview/libvtkPVServerManagerCore.so.1
#13 0x766be015 in vtkSMReaderFactory::CanReadFile(char const*, 
vtkSMProxy*) () from /usr/lib/paraview/libvtkPVServerManagerCore.so.1
#14 0x766bec91 in 
vtkSMReaderFactory::vtkInternals::vtkValue::CanReadFile(char const*, 
std::vector, std::allocator > > const&, vtkSMSession*, bool) 
() from /usr/lib/paraview/libvtkPVServerManagerCore.so.1
#15 0x766bf0fc in vtkSMReaderFactory::GetPossibleReaders(char const*, 
vtkSMSession*) () from /usr/lib/paraview/libvtkPVServerManagerCore.so.1
#16 0x773e067f in pqSelectReaderDialog::pqSelectReaderDialog(QString 
const&, pqServer*, vtkSMReaderFactory*, QWidget*) () from 
/usr/lib/paraview/libvtkpqComponents.so.1
#17 0x77ab2d5d in pqLoadDataReaction::DetermineFileReader(QString 
const&, pqServer*, vtkSMReaderFactory*, QPair&) () from 
/usr/lib/paraview/libvtkpqApplicationComponents.so.1
#18 0x77ab3bd5 in pqLoadDataReaction::loadData(QList 
const&) () from /usr/lib/paraview/libvtkpqApplicationComponents.so.1
#19 0x77ab48bf in pqLoadDataReaction::loadData(QStringList const&) () 
from /usr/lib/paraview/libvtkpqApplicationComponents.so.1
#20 0x77a82c3d in 
pqCommandLineOptionsBehavior::processCommandLineOptions() () from 
/usr/lib/paraview/libvtkpqApplicationComponents.so.1
#21 0x752246a0 in QMetaObject::activate(QObject*, QMetaObject const*, 
int, void**) () from /usr/lib/x86_64-linux-gnu/libQtCore.so.4
#22 0x7522eefa in ?? () from /usr/lib/x86_64-linux-gnu/libQtCore.so.4
#23 0x7522a293 in QObject::event(QEvent*) () from 
/usr/lib/x86_64-linux-gnu/libQtCore.so.4
#24 0x7573c54c in QApplicationPrivate::notify_helper(QObject*, QEvent*) 
() from /usr/lib/x86_64-linux-gnu/libQtGui.so.4
#25 0x7574352c in QApplication::notify(QObject*, QEvent*) () from 
/usr/lib/x86_64-linux-gnu/libQtGui.so.4
#26 0x7520ff5d in QCoreApplication::notifyInternal(QObject*, QEvent*) 
() from /usr/lib/x86_64-linux-gnu/libQtCore.so.4
#27 0x75242d20 in ?? () from /usr/lib/x86_64-linux-gnu/libQtCore.so.4
#28 0x7523ff21 in ?? () from /usr/lib/x86_64-linux-gnu/libQtCore.so.4
#29 0x7fffe9bd37d7 in g_main_context_dispatch () from 
/lib/x86_64-linux-gnu/libglib-2.0.so.0
#30 0x7fffe9bd3a40 in ?? () from /lib/x86_64-linux-gnu/libglib-2.0.so.0
#31 0x7fffe9bd3aec in g_main_context_iteration () from 
/lib/x86_64-linux-gnu/libglib-2.0.so.0
#32 0x75240894 in 
QEventDispatcherGlib::processEvents(QFlags) () 
from /usr/lib/x86_64-linux-gnu/libQtCore.so.4
#33 0x757e65d6 in ?? () from /usr/lib/x86_64-linux-gnu/libQtGui.so.4
#34 0x7520e82f in 

Bug#726775: libslepc3.4.2-dev: CMake script location

[Drew Parsons]

SLEPcConfig.cmake is no longer provided by SLEPc (3.7).

There is a internal script at 
/usr/lib/slepcdir/3.7.3/x86_64-linux-gnu-real/lib/slepc/conf/SLEPcBuildInternal.cmake

But it is used only for the internal build, it's not intended to be
used by client programs.

slepc4py uses the SLEPC_DIR mechanism to work out build flags.  dolfin
provides its own cmake/modules/FindSLEPc.cmake (again using SLEPC_DIR).
 

Upstream intends that pkgconfig be used instead. It's much simpler than
cmake.  SLEPc.pc is installed in /usr/lib/pkgconfig/ (the preferred
version is controlled by alternatives)

Actually I should probably make that 
/usr/lib/x86_64-linux-gnu/pkgconfig/
so I'll leave this bug open until I sort that out.

The same applies to PETSc.

Drew

On Sat, 19 Oct 2013 01:32:50 +0200 =?utf-
8?q?Torquil_Macdonald_S=C3=B8rensen?=  wrote:
> Package: libslepc3.4.2-dev
> Version: 3.4.2.dfsg-1
> Severity: normal
> 
> libslepc3.4.2-dev includes a file , which must be
> a cmake script, intended so that find_package(SLEPc) can be used in a
> CMakeLists.txt?
> 
> However, it doesn't seem to be placed in a directory that is in
> the search path of cmake, so perhaps it ought to be moved somewhere
> else?
> 

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Bug#822971: dolfin: FTBFS on kfreebsd

[Drew Parsons]

On Sat, 17 Sep 2016 11:29:54 +0800 Drew Parsons <dpars...@debian.org>
wrote:
> ... It's not yet built at the moment due to
> other build-dependencies higher up the chain.

Specifically, mpi4py (python-mpi4py) is not currently building on
kfreebsd.

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Bug#822971: dolfin: FTBFS on kfreebsd

[Drew Parsons]

On Fri, 29 Apr 2016 13:46:07 + Mattia Rizzolo 
wrote:
> 
> Since this version, with the switch to vtk6 and whatnot, dolfin FTBFS
on
> kfreebsd.

Looks like this was a transient failure.  dolfin later built
successfully in kfreebsd.  It's not yet built at the moment due to
other build-dependencies higher up the chain.  I'll wait for that to
clear before closing this bug.

Drew

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Re: dolfin_2016.1.0-4_source.changes ACCEPTED into unstable

[Drew Parsons]

On Wed, 2016-09-14 at 09:56 +0200, Johannes Ring wrote:
> Hi Drew,
> Changes:
> >  dolfin (2016.1.0-4) unstable; urgency=medium
> >  .
> >    * Disable HDF5 support.
> > 
> Can you give more details about the error? I think this might be a
> bug
> in the FindHDF5.cmake file in CMake. Did you see this problem with
> version 3.6.1 or 3.6.2 of CMake? Or both? There was a regression in
> version 3.6.1 that was fixed in 3.6.2 as can be seen here:
> 
> https://cmake.org/gitweb?p=cmake.git;a=commit;h=b61eab249f6d119e6353c
> 02c4c79ccb15a3825b9
> https://blog.kitware.com/cmake-3-6-2-available-for-download/
> 
> It would be good if we can re-enable HDF5 support again once this is
> fixed.

Hi Johannes,  I agree, it would be good to have HDF5 support. 
Note that we've never actually had it. It was enabled in the configure
line but got disabled during configure.  Historical build logs are at 
https://buildd.debian.org/status/logs.php?pkg=dolfin=amd64
and
https://buildd.debian.org/status/package.php?p=dolfin

The problem seems to be come from the 2 versions of hdf5,
libhdf5-mpi-dev (parallel) and libhdf5-dev (serial).  We want dolfin to
use libhdf5-mpi-dev but libhdf5-dev is pulled in by libarmadillo-dev
via libvtk6-dev.

So both versions of hdf5 are installed simultaneously. dolfin detects
the serial version and complains that it's not consistent with the
parallel CXX that it found.  Previously dolfin just disabled HDF5 at
that point.  But now (possibly due to updates in the hdf5 packages)
it's started keeping HDF5 enabled. But then it's confused about the
parallel version. It wants to access H5Pset_dxpl_mpio which is only
defined in parallel HDF5, but it's using the serial HDF5 libraries. So
the build now fails against H5Pset_dxpl_mpio (at least, until I
disabled HDF5).

I've put some more detail into the git commit, 
https://anonscm.debian.org/git/debian-science/packages/fenics/dolfin.git/commit/?id=5ccf048ccb4fd7f98aff26fd072787cbe750afea

Another nuance is that parallel HDF5 provides parallel-aware compiler
wrappers, h5pcc (C) and h5pfc (fortran), but there is no h5pc++ or
h5pcxx for C++.

Part of the problem is that FindHDF5.cmake currently looks for h5pc++
or h5c++, which breaks discovery of parallel HDF5 since there is no
h5pc++.

Perhaps it could help if FindHDF5.cmake used the HDF5 pkgconfig files.
 The default is /usr/lib//pkgconfig/hdf5.pc
which doesn't help since it could be either hdf5-serial.pc or
hdf5-openmpi.pc (or hdf5-mpich.pc), controlled by update-alternatives.
But FindHDF5.cmake could look for the mpi or the serial version, or
have the .pc file provided as a configure option.

hdf5-openmpi.pc gives Cflags but no CXXflags. I'm not certain if that
would be enough, but "-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi -lhdf5"
would fix the build failure I think.






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Bug#836677: FTBFS: superlu not needed for superlu 5.2

[Drew Parsons]

retitle 836677 FTBFS: superlu patch needs updating for superlu 5.2
thanks

On Sun, 04 Sep 2016 23:59:19 +0800 Drew Parsons <dpars...@debian.org>
wrote:
> 
> pysparse FTBFS against libsuperlu-dev 5.2, with the error:
> 
>   In file included from Src/superlu3module.c:12:0:
>   /usr/include/superlu/slu_ddefs.h:151:16: note: expected ‘SuperLUStat_t * 
>{aka struct  *}’ but argument is of type ‘int *’
>extern voiddgstrf (superlu_options_t*, SuperMatrix*,
>   ^~
>   Src/superlu3module.c:270:3: error: too few arguments to function 
>‘dgstrf’
>  dgstrf(>options, , relax, panel_size,
>  ^~
> 
... 
> I don't know what's going on between superlu 4.3 and 5.2 with respect
> to dgstrf, but if superlu-4.3.patch is not applied, then the build
> of pysparse against superlu 5.2 does complete successfully.
> 

The clue is the warning that precedes the error: "expected
‘SuperLUStat_t *’ but argument is of type ‘int *’

In /usr/include/superlu/slu_ddefs.h for superlu 5.2, a new
SuperLUStat_t* argument for dgstrf is inserted at the end just before
the final int* argument.

So even though the right number of arguments is present when the
superlu patch is deactivated, they're not the right arguments.  Almost
certainly any application using pysparse built without a patch for
superlu 5.2 would crash at runtime. 

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Bug#836677: FTBFS: superlu not needed for superlu 5.2

[Drew Parsons]

Source: pysparse
Version: 1.1-1.3
Severity: important

superlu 5.2 is currently in experimental but will soon be released to
unstable.

pysparse FTBFS against libsuperlu-dev 5.2, with the error:

  In file included from Src/superlu3module.c:12:0:
  /usr/include/superlu/slu_ddefs.h:151:16: note: expected ‘SuperLUStat_t * {aka 
struct  *}’ but argument is of type ‘int *’
   extern voiddgstrf (superlu_options_t*, SuperMatrix*,
  ^~
  Src/superlu3module.c:270:3: error: too few arguments to function ‘dgstrf’
 dgstrf(>options, , relax, panel_size,
 ^~


Curiously, debian/patches/superlu-4.3.patch is the one that removes an
argument to dgstrf.

I don't know what's going on between superlu 4.3 and 5.2 with respect
to dgstrf, but if superlu-4.3.patch is not applied, then the build
of pysparse against superlu 5.2 does complete successfully.

The bug is no more severe than "important" while superlu 5.2 is in
experimental, but will become serious once it is released to unstable.


-- System Information:
Debian Release: stretch/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.7.0-1-amd64 (SMP w/8 CPU cores)
Locale: LANG=en_AU.utf8, LC_CTYPE=en_AU.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

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Bug#827740: Re #827740: isympy start fails: No module named sympy.interactive

[Drew Parsons]

On Mon, 20 Jun 2016 14:06:11 +0200 Alberto Luaces 
wrote:
>  Maybe another binary package could be added (named isympy3),
> including
>  an appropriate isympy3 script...
>  At that point isympy would depend on python-sympy (without
>  python3-sympy as an alternative dependency) and isympy3 would
> depend on
>  python3-sympy.
> 
> I guess a good solution could be one along the lines you are posting:
> having two packages with no intermixed dependencies, with some aid of
> the dpkg alternative system (that is used, for example, to set the
> default version of gcc).  Unfortunately, I currently do not know
> enough
> of that system in order to send a patch right now.


Alternatives won't provide a clean fix, although we should be able to
make some kind of isympy3 work.

Because of the shebang,  calling isympy directly (rather than via
python isympy or python3 isympy) will always load python2.

Luke's patch removes the option of using isympy with python3, but we
shouldn't need to do that.

Seems to me the best option is to create as separate isympy3 script
(with a separate isympy3 package) which does nothing other than call
python3 isympy.

I'll load a patch to git.

Drew

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Bug#754390: #754390: [src:slepc] any chance to backport more current version to wheezy-backports?

[Drew Parsons]

Hi Giacomo, which version of stable are you currently using? Not wheezy
at the moment?

The current petsc in unstable/testing is 3.6.4 (soon to be updated to
3.7). slepc is closely bound to petsc of course (also v3.6 moving soon
to 3.7)

wheezy fails on these petsc build-depends:
  mpi-default-dev (>= 1.0.2) (wheezy has 1.0.1)
  libsuitesparse-dev (>= 1:4.2.1)  (wheezy has 1:3.4.0-3)

These differences make it difficult (in terms of developer time
resources) to backport.  But if you have the time, it should be
possible for you to hack the build scripts, debian/control and
debian/rules.  For instance you could remove support for suitesparse.   

petsc 3.6.4.dfsg1-3 does build fine on jessie.  You should be able to
build a custom deb package without too much trouble:
  apt-get build-dep petsc
  apt-get install pkg-config libssl-dev   # new build-deps
Download the new petsc source, e.g. the 3 source files listed at 
https://packages.debian.org/source/sid/petsc
Unpack:
  dpkg-source -x petsc_3.6.4.dfsg1-3.dsc
Enter the petsc source dir and build the packages with
  dpkg-buildpackage
or
  dpkg-buildpackage 2>&1 | tee ../build.log

If petsc builds fine then the analogous steps should allow slepc to
build too.

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