Accepted vnlog 1.6-1 (source amd64 all) into unstable

[Dima Kogan]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sun, 01 Apr 2018 22:14:38 -0700
Source: vnlog
Binary: libvnlog0 libvnlog-dev vnlog libvnlog-perl python-vnlog python3-vnlog
Architecture: source amd64 all
Version: 1.6-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Dima Kogan <dko...@debian.org>
Description:
 libvnlog-dev - Toolkit to read/write/manipulate whitespace-separated ASCII logs
 libvnlog-perl - Toolkit to read/write/manipulate whitespace-separated ASCII 
logs
 libvnlog0  - Toolkit to read/write/manipulate whitespace-separated ASCII logs
 python-vnlog - Toolkit to read/write/manipulate whitespace-separated ASCII logs
 python3-vnlog - Toolkit to read/write/manipulate whitespace-separated ASCII 
logs
 vnlog  - Toolkit to read/write/manipulate whitespace-separated ASCII logs
Changes:
 vnlog (1.6-1) unstable; urgency=medium
 .
   * New upstream release. C library works on armhf, armel
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Re: Comments regarding vnlog_1.5-1_amd64.changes

[Dima Kogan]

Chris Lamb  writes:

> Just add that he is the author? I mean, just to give some kind of
> credit...

Alrighty. Done.

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Re: Comments regarding vnlog_1.5-1_amd64.changes

[Dima Kogan]

Chris Lamb  writes:

> Hi, would be nice to attribute credit to Chris Venter for
> b64_encode.c, even if not necessary :)
>
>  -- Chris Lamb   Sun, 01 Apr 2018 10:09:43 +

Hi. Thanks for pushing this through NEW so quickly. I acknowledge Chris
Venter's copyright in the README. What would you suggest for a better
attribution?

dima

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Accepted feedgnuplot 1.49-1 (source all) into unstable

[Dima Kogan]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Fri, 16 Mar 2018 13:56:27 -0700
Source: feedgnuplot
Binary: feedgnuplot
Architecture: source all
Version: 1.49-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Dima Kogan <dko...@debian.org>
Description:
 feedgnuplot - Pipe-oriented frontend to Gnuplot
Changes:
 feedgnuplot (1.49-1) unstable; urgency=medium
 .
   * --vnl now works with plots that have rangesize > 1
   * zsh completion: --xlen argument isn't optional
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Accepted vlfeat 0.9.21+dfsg0-1 (source amd64 all) into unstable

[Dima Kogan]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Fri, 02 Mar 2018 23:23:30 -0800
Source: vlfeat
Binary: libvlfeat1 libvlfeat-dev libvlfeat-doc octave-vlfeat
Architecture: source amd64 all
Version: 0.9.21+dfsg0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Dima Kogan <dko...@debian.org>
Description:
 libvlfeat-dev - Computer vision library focussing on visual features and 
clusteri
 libvlfeat-doc - Computer vision library focussing on visual features and 
clusteri
 libvlfeat1 - Computer vision library focussing on visual features and clusteri
 octave-vlfeat - Computer vision library focussing on visual features and 
clusteri
Closes: 816397
Changes:
 vlfeat (0.9.21+dfsg0-1) unstable; urgency=medium
 .
   * New upstream release
   * Added a note highlighting removal of patented code (Closes: #816397)
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Accepted feedgnuplot 1.48-1 (source all) into unstable

[Dima Kogan]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sat, 24 Feb 2018 12:56:05 -0800
Source: feedgnuplot
Binary: feedgnuplot
Architecture: source all
Version: 1.48-1
Distribution: sid
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Dima Kogan <dko...@debian.org>
Description:
 feedgnuplot - Pipe-oriented frontend to Gnuplot
Changes:
 feedgnuplot (1.48-1) unstable; urgency=medium
 .
   * Added --tuplesize and --tuplesizeall
   * vnlog integration
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Accepted libdogleg 0.14-1 (source amd64 all) into unstable

[Dima Kogan]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Mon, 12 Feb 2018 23:16:29 -0800
Source: libdogleg
Binary: libdogleg2 libdogleg-doc libdogleg-dev
Architecture: source amd64 all
Version: 0.14-1
Distribution: sid
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Dima Kogan <dko...@debian.org>
Description:
 libdogleg-dev - Powell's dog-leg nonlinear least squares solver for sparse 
matric
 libdogleg-doc - Powell's dog-leg nonlinear least squares solver for sparse 
matric
 libdogleg2 - Powell's dog-leg nonlinear least squares solver for sparse matric
Changes:
 libdogleg (0.14-1) unstable; urgency=medium
 .
   * Minor upstream update
 - gradient-testing reports are now printed in an easy-to-parse asciilog
 - CHOLMOD error callback now uses the standardized wrapped print
Checksums-Sha1:
 de127c1fa886b78b59c88bc5701c0dbbd144ab94 2166 libdogleg_0.14-1.dsc
 48e6c69b80878066af3eb6d3ab8ae1d7286dc470 20991 libdogleg_0.14.orig.tar.gz
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 f22b3b9c7882cbed96caaa250ca301172de39b8a 14880 libdogleg-dev_0.14-1_amd64.deb
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 9e6134a630a745297162014f058d488936cbe32c2182a3cbfe42d5e673e5f1b3 20991 
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 bf2d71773e7aeb99957c252221403806333ccae5f0baad03f307397d63c23550 24008 
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 8bfcebdf7a00ab86a8bfeac878e7745d496093f4a37ae63ddf915b2daecbe842 6915 
libdogleg_0.14-1_amd64.buildinfo
Files:
 80af15d94129e6faf2c1776988fe75af 2166 science optional libdogleg_0.14-1.dsc
 7c739ec6743ede2773bdaf44ed0d0ca0 20991 science optional 
libdogleg_0.14.orig.tar.gz
 f8b5a549ad4baa335d18f862cc01ef19 2920 science optional 
libdogleg_0.14-1.debian.tar.xz
 b8bad767eba613ddea4a4e8152e86351 14880 libdevel optional 
libdogleg-dev_0.14-1_amd64.deb
 ae1046aa95b3a768265215c989635074 21784 doc optional 
libdogleg-doc_0.14-1_all.deb
 36660a17dec4cc9c6a11f2ca0f2cec63 24008 debug optional 
libdogleg2-dbgsym_0.14-1_amd64.deb
 03550b6b01121d58933773205839e02a 13452 libs optional 
libdogleg2_0.14-1_amd64.deb
 be4c80b2fd8bca1c2048fc341433d6da 6915 science optional 
libdogleg_0.14-1_amd64.buildinfo

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Bug#876300: libsundials-dev: libsundials-serial-dev is gone

[Dima Kogan]

Thanks for the report


Paolo Greppi  writes:

> on stretch libsundials-serial-dev is available.
>
> With the update 2.7.0 release this is not available anymore. I assume it
> is replaced by libsundials-dev.

Yep


> Should there be a transitional package to ease the migration ?

There's nothing that depends on libsundials-serial-dev, so it's not
obvious to me we need a migration package. Why do you think we need it?


dima

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Bug#883619: libceres-dev: dependency on libeigen3-dev isn't strong enough

[Dima Kogan]

Package: libceres-dev
Version: 1.13.0+dfsg0-1
Severity: normal

Hi. Currently in libceres-dev we have

  Depends: libeigen3-dev (>= 3.2.1)

However in /usr/lib/cmake/Ceres/CeresConfig.cmake it does

  set(CERES_EIGEN_VERSION 3.3.4)

And then proceeds to barf if this wasn't found. The Depends should be
tightened accordingly, or the requirement in the .cmake file should be
loosened, if it CAN work with < 3.3.4.

Thanks

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Re: sundials_2.7.0+dfsg-1~exp1_amd64.changes REJECTED

[Dima Kogan]

Chris Lamb  writes:

> Looks like a bunch of missing attributions under examples/templates/*
> and config/.

Thanks for finding these. Did you do this manually, or do you have some
tool to check debian/copyright for completeness?

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Bug#770290: libblas3: please convert to multiarch

[Dima Kogan]

S�bastien Villemot <sebast...@debian.org> writes:

> Le lundi 20 mars 2017 � 00:12 -0700, Dima Kogan a �crit:
>
>> I'm attaching a patch series that applies this idea here. The patches
>> mostly work. There're at least two bugs here that need to be dealt
>> with, and I can work on those. But in the meantime, let's decide that
>> this is the approach we want to pursue.
>
> I agree with the general approach, and I have committed your patches on
> a new git branch named "multiarch".

Cool!


> I have also added two commits, for fixing a bug in your patches, and
> for removing the libblas-common package which will be obsoleted by this
> move.
>
>> 2. There's now a separate set of alternatives for each arch called
>> something like blas-ARCH. Installing one of the new packages creates
>> these new alternatives, but doesn't remove the old alternatives,
>> which end up as a broken link.
>
> Indeed. If you have time, don't hesitate to provide a patch (or even
> better, to commit it directly to the git branch).

OK. I'll take a look at some point.


>> Clearly, we'd also need to update the other packages that provide
>> BLAS implementations, but let's do this one step at a time.
>
> Indeed, once we have agreed on an implementation for lapack, we need to
> apply similar changes to openblas and atlas, and also add versioned
> breaks between the various packages (to avoid coexistence of the old
> and the new alternatives system).
>
> Then we will do a simultaneous upload of the 3 packages, first to
> experimental.

Great. I have two more patches (attached), that were needed for
cross-building.

>From 468609426ab37e7c64170443e20b6baa77d1d51c Mon Sep 17 00:00:00 2001
From: Dima Kogan <dko...@debian.org>
Date: Sat, 6 May 2017 21:01:41 -0700
Subject: [PATCH 1/3] using arch-specific compilers, binutils

---
 debian/patches/series  |  1 +
 debian/patches/using-arch-specific-compilers.patch | 39 ++
 debian/rules   |  6 ++--
 3 files changed, 43 insertions(+), 3 deletions(-)
 create mode 100644 debian/patches/using-arch-specific-compilers.patch

diff --git a/debian/patches/series b/debian/patches/series
index e396170..3130da1 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,4 @@ icamax-izamax-extended-precision.patch
 doxygen-strip-source.patch
 fix-typos.patch
 test-numbering.patch
+using-arch-specific-compilers.patch
diff --git a/debian/patches/using-arch-specific-compilers.patch b/debian/patches/using-arch-specific-compilers.patch
new file mode 100644
index 000..7ba01a8
--- /dev/null
+++ b/debian/patches/using-arch-specific-compilers.patch
@@ -0,0 +1,39 @@
+diff --git a/INSTALL/make.inc.gfortran b/INSTALL/make.inc.gfortran
+index ccd0994..1c5bd62 100644
+--- a/INSTALL/make.inc.gfortran
 b/INSTALL/make.inc.gfortran
+@@ -16,11 +16,11 @@ SHELL = /bin/sh
+ #  and handle these quantities appropriately. As a consequence, one
+ #  should not compile LAPACK with flags such as -ffpe-trap=overflow.
+ #
+-FORTRAN  = gfortran
++FORTRAN  = $(DEB_HOST_GNU_TYPE)-gfortran
+ OPTS = -O2 -frecursive
+ DRVOPTS  = $(OPTS)
+ NOOPT= -O0 -frecursive
+-LOADER   = gfortran
++LOADER   = $(DEB_HOST_GNU_TYPE)-gfortran
+ LOADOPTS =
+ #
+ # Timer for the SECOND and DSECND routines
+@@ -46,7 +46,7 @@ TIMER= INT_ETIME
+ #
+ # CC is the C compiler, normally invoked with options CFLAGS.
+ #
+-CC = gcc
++CC = $(DEB_HOST_GNU_TYPE)-gcc
+ CFLAGS = -O3
+ #
+ # LAPACKE has also the interface to some routines from tmglib,
+@@ -56,9 +56,9 @@ CFLAGS = -O3
+ #  The archiver and the flag(s) to use when building archive (library)
+ #  If you system has no ranlib, set RANLIB = echo.
+ #
+-ARCH = ar
++ARCH = $(DEB_HOST_GNU_TYPE)-ar
+ ARCHFLAGS= cr
+-RANLIB   = ranlib
++RANLIB   = $(DEB_HOST_GNU_TYPE)-ranlib
+ #
+ #  Location of the extended-precision BLAS (XBLAS) Fortran library
+ #  used for building and testing extended-precision routines.  The
diff --git a/debian/rules b/debian/rules
index d917bbf..e4c0f6a 100755
--- a/debian/rules
+++ b/debian/rules
@@ -12,11 +12,11 @@ SO:=3
 BUILDFLAGS_ENV:=DEB_LDFLAGS_MAINT_STRIP="-Wl,-Bsymbolic-functions"
 LDFLAGS:=$(shell $(BUILDFLAGS_ENV) dpkg-buildflags --get LDFLAGS)
 
-F77:=gfortran
+F77:=$(DEB_HOST_GNU_TYPE)-gfortran
 FFLAGS:=$(shell dpkg-buildflags --get FFLAGS)
 FFLAGS_NOOPT:=$(shell DEB_BUILD_OPTIONS=noopt dpkg-buildflags --get FFLAGS)
 
-CC:=/usr/bin/cc
+CC:=$(DEB_HOST_GNU_TYPE)-gcc
 CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
 CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
 
@@ -53,7 +53,7 @@ endif
 	dh $@
 
 make.inc: INSTALL/make.inc.gfortran
-	sed -e "s,\(^CC  *=\).*,\1 /usr/bin/cc,1" \
+	sed -e "s,\(^CC  *=\).*,\1 $(DEB_HOST_GNU_TYPE)-gcc,1" \
 	-e "s,\(^NOOPT  *=\).*,\1 \$$(PICOPTS) $(FFLAGS_

Re: sundials_2.7.0+dfsg-1~1_amd64.changes REJECTED

[Dima Kogan]

Andreas Tille <andr...@an3as.eu> writes:

> On Mon, May 22, 2017 at 12:17:58AM -0700, Dima Kogan wrote:
>> > My plan is to work on it this weekend. Do keep pinging me to make sure
>> > it's done.
>>
>> Progress. All examples now build from /usr/share/doc. This is the main
>> remaining technical hurdle. The rest is important, but shouldn't take
>> terribly long to complete.
>
> Thanks a lot for the update.  It would be nice if you would push your
> changes to Git - may be I could check in advance.

I pushed it yesterday to

  ssh://git.debian.org/git/debian-science/packages/sundials.git

Dependencies are almost certainly incomplete still. There's a single
-dev package, and the examples are all in -doc, which will change.
Still, Each example (after gunzipping) builds with

  cmake -Wno-dev && make

All testing and fixes appreciated.

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Re: sundials_2.7.0+dfsg-1~1_amd64.changes REJECTED

[Dima Kogan]

Andreas Tille  writes:

> any news from this package?

My plan is to work on it this weekend. Do keep pinging me to make sure
it's done.

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Bug#861988: src:cminpack: DEB_BUILD_OPTIONS=nocheck is now supported

[Dima Kogan]

Package: src:cminpack
Severity: normal
Hi. The package sources weren't respecting DEB_BUILD_OPTIONS=nocheck.
That attached patch fixes this.

Thanks!

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

Kernel: Linux 4.8.0-2-amd64 (SMP w/2 CPU cores)
Locale: LANG=C, LC_CTYPE=C (charmap=ANSI_X3.4-1968) (ignored: LC_ALL set to C)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

>From dee932e4c54aabb24ba4e0d2d388285082fdbb52 Mon Sep 17 00:00:00 2001
From: Dima Kogan <dko...@debian.org>
Date: Sat, 6 May 2017 19:22:46 -0700
Subject: [PATCH] explicitly supporting DEB_BUILD_OPTIONS=nocheck

override_dh_auto_test ALWAYS runs, it's up to the thing being executed to
respect DEB_BUILD_OPTIONS=nocheck
---
 debian/rules | 5 +
 1 file changed, 5 insertions(+)

diff --git a/debian/rules b/debian/rules
index dc8ea3d..d75f194 100755
--- a/debian/rules
+++ b/debian/rules
@@ -16,7 +16,12 @@ override_dh_auto_configure:
 	dh_auto_configure -- $(CMAKE_EXTRA_FLAGS)
 
 override_dh_auto_test:
+ifeq ($(filter $(DEB_BUILD_OPTIONS),nocheck),)
 	$(MAKE) -C examples ctest
+else
+	@echo '"DEB_BUILD_OPTIONS" has "nocheck". Skipping tests'
+	true
+endif
 
 override_dh_clean:
 	dh_clean
-- 
2.11.0

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Re: sundials_2.7.0+dfsg-1~1_amd64.changes REJECTED

[Dima Kogan]

Dima Kogan <d...@secretsauce.net> writes:

> OK. It's nowhere near done, but probably good enough for experimental.
> Give me a few days.

I just looked at it. There actually are some package names that are new
in respect with the previous packages and that probably will change when
we actually finish this (specifically libsundials-dev and
libsundials-doc). I think I don't want anything going into NEW that will
disappear by the time we make a non-experimental release. So let's hold
off. Yes? The tree in git can be used to build packages. You mentioned
that an upload would be useful for testing packages that

Depends:libsundials-something

Are there specific ones you're thinking of?

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Re: sundials_2.7.0+dfsg-1~1_amd64.changes REJECTED

[Dima Kogan]

On April 13, 2017 4:55:23 AM PDT, Andreas Tille  wrote:
>
>I wonder whether you think the package names will need some change.  If
>not I think it might make sense to push again to experimental to let it
>pass new queue.  Users should assume that packages in experimental are
>... well, just experimental.  My motivation to suggest this upload is
>that while I fully agree that the examples should work I could in
>parallel check whether other libs needing this library will build.  I
>could concentrate on my initial target and while doing so doing
>parallel
>tests

OK. It's nowhere near done, but probably good enough for experimental. Give me 
a few days.


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Re: sundials_2.7.0+dfsg-1~1_amd64.changes REJECTED

[Dima Kogan]

Andreas Tille  writes:

> Please let me know if any help might be needed. New queue is currently
> very short - so this might be a good time for uploading.

Hi. Before trying to upload again, I'd like to actually get this into a
state when I myself know that it's semi-working. My benchmark is that I
should be able to

- install the packages
- build the examples from the packages
- run the examples I just built

I worked on it a bit last week, and it's in much better shape now, but
still not upload-worthy, I think. I talked to James Tocknell about
progress to coordinate with him, but I don't think he had the cycles to
do anything here.

The current state of the tree in master:

- All the various nvec types split into separate packages. All the
  different PARALLEL types split into separate packages

- A single libsundials-dev does everything. This probably is wrong, but
  is good enough to test. Let's get everything else right, then split
  this

- debian/control has bogus descriptions and dependencies

- I'm not building examples WHEN BUILDING THE PACKAGES, but instead I'm
  shipping them in libsundials-doc (should instead go into the -dev
  package of whatever is being demonstrated). The user should be able to

1. cd /usr/share/doc/whatever/examples
2. mkdir build
3. cd build
4. cmake ..
5. make
6. run example

  This required some patching to the example cmake files (I've only
  touched arkode for now), but this now works at least for
  arkode/C_serial

  Once we're happy with how this is done, we can apply these patches to
  all the examples

- The pkgconfig business for PETSc wasn't working. Rather pkg-config
  itself was working, but cmake was being stupid and doing something
  wrong with the results. It took me way too long to debug it, and I
  never did figure it out. But we have Build-depends, so we don't need
  to find anything: we already know where everything is. Thus the
  current makefiles simply take the output of pkg-config and don't test
  it. If somebody wants to fix that, go for it.


In any case, the packages are building are working somewhat. I'll pick
this up again when I have the cycles, but if somebody wants to push on
it before then, PLEASE do so!

dima

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Re: sundials_2.7.0+dfsg-1~1_amd64.changes REJECTED

[Dima Kogan]

Thorsten Alteholz  writes:

> as I didn't find the depedency mpi-default-run in the archive, I
> assume that this is a typo. Please reupload the package if I missed it
> somewhere ...

Hi. Thanks much for checking this. These packages are not ready for
primetime (hence going to experimental), but I thought they were
installable at least. I'll clean them up as I get the time and
reuploaded something when it's ready.

dima

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Bug#770290: ping

[Dima Kogan]

Hi. Can we get this working? There're many packages that

  Build-Depends: (stuff that eventually depends on BLAS)

and those can't be cross-built right now.

The main proposal from #760936 was to manage a separate alternative for
each architecture. There's precedent for this at least in src:petsc and
src:s2tc.

I'm attaching a patch series that applies this idea here. The patches
mostly work. There're at least two bugs here that need to be dealt with,
and I can work on those. But in the meantime, let's decide that this is
the approach we want to pursue. The issues:


1. Something is wrong with libblas.a. It ends up mostly empty for me

2. There's now a separate set of alternatives for each arch called
something like blas-ARCH. Installing one of the new packages creates
these new alternatives, but doesn't remove the old alternatives, which
end up as a broken link.


Clearly, we'd also need to update the other packages that provide BLAS
implementations, but let's do this one step at a time.

dima
>From 44744e7be2610fb94d14723af356f24d7c3a36c5 Mon Sep 17 00:00:00 2001
From: Dima Kogan <dko...@debian.org>
Date: Sun, 12 Mar 2017 18:23:53 -0700
Subject: [PATCH 1/4] installing everything to an arch-dependent path

---
 debian/control| 2 +-
 debian/libblas-dev.install| 6 --
 debian/libblas3.install   | 4 +++-
 debian/liblapack-dev.install  | 8 +---
 debian/liblapack-pic.install  | 4 +++-
 debian/liblapack3.install | 4 +++-
 debian/liblapacke-dev.install | 6 --
 debian/liblapacke.install | 6 --
 debian/libtmglib-dev.install  | 6 --
 debian/libtmglib3.install | 4 +++-
 10 files changed, 34 insertions(+), 16 deletions(-)
 mode change 100644 => 100755 debian/libblas-dev.install
 mode change 100644 => 100755 debian/libblas3.install
 mode change 100644 => 100755 debian/liblapack-dev.install
 mode change 100644 => 100755 debian/liblapack-pic.install
 mode change 100644 => 100755 debian/liblapack3.install
 mode change 100644 => 100755 debian/liblapacke-dev.install
 mode change 100644 => 100755 debian/liblapacke.install
 mode change 100644 => 100755 debian/libtmglib-dev.install
 mode change 100644 => 100755 debian/libtmglib3.install

diff --git a/debian/control b/debian/control
index 04777f8..0dd314f 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Section: libs
 Priority: optional
 Maintainer: Debian Science Team <debian-science-maintainers@lists.alioth.debian.org>
 Uploaders: Sébastien Villemot <sebast...@debian.org>
-Build-Depends: debhelper (>= 10), gfortran, python, dpkg-dev (>= 1.16.1~)
+Build-Depends: debhelper (>= 10), gfortran, python, dpkg-dev (>= 1.16.1~), dh-exec
 Build-Depends-Indep: doxygen, graphviz
 Standards-Version: 3.9.8
 Homepage: http://www.netlib.org/lapack/
diff --git a/debian/libblas-dev.install b/debian/libblas-dev.install
old mode 100644
new mode 100755
index 58b0a87..e817416
--- a/debian/libblas-dev.install
+++ b/debian/libblas-dev.install
@@ -1,5 +1,7 @@
-libblas.so usr/lib/libblas/
-libblas.a usr/lib/libblas/
+#!/usr/bin/dh-exec
+
+libblas.so usr/lib/${DEB_HOST_MULTIARCH}/libblas/
+libblas.a usr/lib/${DEB_HOST_MULTIARCH}/libblas/
 CBLAS/include/cblas.h usr/include/
 CBLAS/include/cblas_mangling.h usr/include/
 CBLAS/include/cblas_f77.h usr/include/
diff --git a/debian/libblas3.install b/debian/libblas3.install
old mode 100644
new mode 100755
index ded6b76..078cb04
--- a/debian/libblas3.install
+++ b/debian/libblas3.install
@@ -1 +1,3 @@
-libblas.so.* usr/lib/libblas/
+#!/usr/bin/dh-exec
+
+libblas.so.* usr/lib/${DEB_HOST_MULTIARCH}/libblas/
diff --git a/debian/liblapack-dev.install b/debian/liblapack-dev.install
old mode 100644
new mode 100755
index 8672ba0..a91ff19
--- a/debian/liblapack-dev.install
+++ b/debian/liblapack-dev.install
@@ -1,3 +1,5 @@
-liblapack.so usr/lib/lapack/
-liblapack.a usr/lib/lapack/
-lapack-netlib.pc  /usr/lib/pkgconfig
+#!/usr/bin/dh-exec
+
+liblapack.so usr/lib/${DEB_HOST_MULTIARCH}/lapack/
+liblapack.a usr/lib/${DEB_HOST_MULTIARCH}/lapack/
+lapack-netlib.pc  /usr/lib/${DEB_HOST_MULTIARCH}/pkgconfig
diff --git a/debian/liblapack-pic.install b/debian/liblapack-pic.install
old mode 100644
new mode 100755
index 9473332..71a98a4
--- a/debian/liblapack-pic.install
+++ b/debian/liblapack-pic.install
@@ -1 +1,3 @@
-liblapack_pic.a usr/lib/lapack/
+#!/usr/bin/dh-exec
+
+liblapack_pic.a usr/lib/${DEB_HOST_MULTIARCH}/lapack/
diff --git a/debian/liblapack3.install b/debian/liblapack3.install
old mode 100644
new mode 100755
index acd666f..ddd3d32
--- a/debian/liblapack3.install
+++ b/debian/liblapack3.install
@@ -1 +1,3 @@
-liblapack.so.* usr/lib/lapack/
+#!/usr/bin/dh-exec
+
+liblapack.so.* usr/lib/${DEB_HOST_MULTIARCH}/lapack/
diff --git a/debian/liblapacke-dev.install b/debian/liblapacke-dev.install
old mode 100644
new mode 100755
index 0db42f7..053046b
--- a/debian/liblapacke-dev.install
+++ b/debian/liblapacke-dev.install
@@ -1,3 +1

Bug#856705: closed by Ruben Undheim <ruben.undh...@gmail.com> (Bug#856705: fixed in graywolf 0.1.4+20170306gitecee764-1)

[Dima Kogan]

Debian Bug Tracking System  writes:

> This is an automatic notification regarding your Bug report
> which was filed against the src:graywolf package:
>
> #856705: graywolf: License violation
>
> It has been closed by Ruben Undheim .

Thanks for taking care of this. You rock.

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Bug#856705: [dko...@debian.org: Bug#856705: graywolf: License violation]

[Dima Kogan]

Tim Edwards  writes:

> Well, it's pretty clear that the TimberWolf authors at Yale unabashedly
> plaigerized out of Numerical Recipes for their thesis work.  What you
> found is not particularly difficult to work around, as the single-value
> decomposition routines can be found in the GNU Scientific Library and
> should be reasonably easy to substitute.

Hi. Yeah, there're plenty of other (and better) SVD implementations.
They won't be a drop-in replacement, however because numerical recipes
uses a ridiculous matrix storage scheme:

typedef struct {
INTrows ;
INTcolumns ;
DOUBLE **m ;
} YMBOX, *YMPTR ;

I.e. each row (or column) of a matrix is stored in a separate chunk of
(usually dynamically-allocated) memory. This is stupid, and no other
library would do it this way. So to use other implementations you might
need to write a shim to convert formats. If you find a better way,
please let me know.


>  However, it feeds back into other matrix manipulation routines, so I
> cannot be sure how much of that was pulled from Numerical Recipies.
> This looks like finding a needle in a haystack to me. How did you find
> that bit of plaigerized code, and how would I go about flushing out
> any additional plaigerized sections of code?

I came across some other libraries that were doing a similar thing, and
then searched the Debian codebase (http://codesearch.debian.net) for
some unique-looking comments. Here I searched for

You must augment A with extra zero rows

I also searched for some other things that caught some other libraries,
but the above chunk of text is the only one I found in graywolf. What
you can do is to look at functions that use that YMPTR matrix
representation: anything that uses it is a candidate for being plucked
from the book.

Note that for some reason the utility code to support this matrix
representation IS in the public domain, as indicated in numerical
recipes copyright page linked in the bug report.


> I definitely want these out of the code base, especially as GNU
> alternatives are readily available.

Thank you very much.

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Bug#856705: graywolf: License violation

[Dima Kogan]

Source: graywolf
Severity: serious

Hi. graywolf is using some numerical routines from numerical recipes. These
are NOT free software and may not be used in a free software project.

For Debian, you can elide these sources. It would also be great if you
talked to upstream so that they stop violating copyrights also.

Look at Ysvd_decompose) in

  src/Ylib/svd.c

A later version of the book chapter this function came from lives here:

  http://numerical.recipes/webnotes/nr3web2.pdf

You can see many similarities. If you look at the older version of the
book, you will see 100% similarities.

The copyright statement is here:

  http://numerical.recipes/public-domain.html

I haven't done a thorough search, and I can imagine the SVD
implementation isn't the only violation here. It would be great if you
looked more thoroughly.

Thanks

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Bug#856703: visp: License violation

[Dima Kogan]

Source: visp
Severity: serious
Hi. visp is using some numerical routines from numerical recipes. These
are NOT free software and may not be used in a free software project.

For Debian, you can elide these sources. It would also be great if you
talked to upstream so that they stop violating copyrights also.

Look at vpMatrix::svdNr() in

  modules/core/src/math/matrix/vpMatrix_svd.cpp

A later version of the book chapter this function came from lives here:

  http://numerical.recipes/webnotes/nr3web2.pdf

You can see many similarities. If you look at the older version of the
book, you will see 100% similarities.

The copyright statement is here:

  http://numerical.recipes/public-domain.html


I haven't done a thorough search, and the SVD implementation isn't the
only violation here. For instance I also see

  vpMatrix::LUBksb() and vpMatrix::LUDcmp()

but it would be great if you looked more thoroughly.

Thanks

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Bug#854905: Acknowledgement (libpetsc3.7.5-dev: Package uninstallable: libopenmpi-dev dependency unsatisfiable)

[Dima Kogan]

I should say that this is uninstallable in unstable only. stretch is
fine.

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Bug#854905: libpetsc3.7.5-dev: Package uninstallable: libopenmpi-dev dependency unsatisfiable

[Dima Kogan]

Package: libpetsc3.7.5-dev
Severity: grave

Hi. Currently libpetsc3.7.5-dev is uninstallable. Sbuild resolver says:

missing:
 pkg:
  package: libpetsc3.7.5-dev
  version: 3.7.5+dfsg1-4
  architecture: amd64
  unsat-dependency: libopenmpi-dev:amd64 (< 2.0.2~git.20161226)
 depchains:
  -
   depchain:
-
 package: sbuild-build-depends-sundials-dummy
 version: 0.invalid.0
 architecture: amd64
 depends: libpetsc3.7-dev:amd64
-
 package: libpetsc3.7-dev
 version: 3.7.5+dfsg1-4
 architecture: amd64
 depends: libpetsc3.7.5-dev:amd64
 

Which is true, because libpetsc3.7.5-dev has

Depends: libopenmpi-dev (>= 2.0.2~git.20161225),
 libopenmpi-dev (<< 2.0.2~git.20161226)

But the only available libopenmpi-dev is 2.0.2-2

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Bug#827942: src:gnuplot: All packages that give you a functional gnuplot should Provides:gnuplot

[Dima Kogan]

Package: src:gnuplot
Severity: normal

Hi. Today I installed gnuplot5-qt to plot stuff. Then I tried to install
some other package that Depends:gnuplot, and it demanded that I then
install gnuplot5 also. Should this be necessary? I'm thinking that
we should have more Provides tags to make more things work without
requiring extra packages.

So anything that gives you a gnuplot that can make plots
(gnuplot{,5}-{nox,x11,qt}) should Provides:gnuplot. And gnuplot5-*
should Provides:gnuplot5. Does that sound reasonable?

Thanks!
dima

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Bug#811247: pdl: Stored data files unreadable

[Dima Kogan]

Package: pdl
Version: 1:2.007-4+b2
Severity: important

Hi. Current PDL in Debian silently reads old IO::Storable files with
incorrect contents. No error is produced, you just get bogus results in
your piddles. This was fixed over a year ago:

  http://permalink.gmane.org/gmane.comp.lang.perl.pdl.devel/5644

And the fix was released upstream long ago as well. Can we please update
to the latest upstream release to fix major bugs such as this?

Thanks.

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Bug#784117: qhull-bin: manpages refer to the wrong location for the docs

[Dima Kogan]

Package: qhull-bin
Version: 2012.1-5
Severity: normal

Hi. The manpage for qvoronoi (and others) says

This program is documented fully in HTML
format, file:///usr/share/doc/libqhull-dev/html/
qvoronoi.htm available in the libqhull-dev package.

SEE ALSO
/usr/share/doc/libqhull-dev/html/qvoronoi.htm

This is incorrect. The docs live in libqhull-doc, not libqhull-dev

-- System Information:
Debian Release: 8.0
  APT prefers unstable
  APT policy: (800, 'unstable'), (700, 'testing'), (500, 'stable'), (1, 
'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: armhf, armel, i386

Kernel: Linux 3.16-3-amd64 (SMP w/2 CPU cores)
Locale: LANG=C, LC_CTYPE=C (charmap=ANSI_X3.4-1968) (ignored: LC_ALL set to C)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages qhull-bin depends on:
ii  libc6  2.19-17
ii  libqhull6  2012.1-5

qhull-bin recommends no packages.

Versions of packages qhull-bin suggests:
pn  geomview  none

-- no debconf information

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Bug#756222: update

[Dima Kogan]

I haven't heard anything more about the armhf issue, so I'm going to
ignore it without any more complaints. The not-found .d files is fixed
in an imminent upload

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Bug#756222: src:vlfeat: appears to ignore errors from mkoctfile

[Dima Kogan]

Hi.

This is two separate issues. First the easy one:

The No such file or directory errors you are seeing on amd64 are
benign; the generated packages are not negatively affected. The issue is
that the mkoctfile tool changed its behavior from liboctave-dev 3.6.x
(in stable) to liboctave-dev 3.8.x (testing, unstable). In 3.6.x

 mkoctfile -M SOMEDIR/SOMEFILE.c

would create SOMEDIR/SOMEFILE.d. This is the behavior vlfeat was
assuming. In 3.8.x SOMEFILE.d is created in the current directory
instead. I'll fix it when I update this package, but its benign in the
meantime.



The issue you're seeing on armhf looks more serious, but I don't have
porterbox access, so I can't debug it directly. Looking at the armhf
package in the archive, it looks fine. Looking at the buildd logs that
produced the packages in the archive, it looks fine too:

 
https://buildd.debian.org/status/fetch.php?pkg=vlfeatarch=armhfver=0.9.17%2Bdfsg0-6%2Bb1stamp=1393709508

Here you can see that things built just fine on armhf, including the
mkoctfile commands. Could you simply be running out of memory, and the
slowness is simply swapping?

If you want, you can run the command in your bug report by itself on
your armhf box to see if it is problematic. The command is

 /usr/bin/mkoctfile -I. -I./toolbox -M ./toolbox/slic/vl_slic.c

Run that from the root of the vlfeat tree. If you see the issues
(std::bad_alloc or slowness), then you can try to see if you're hitting
memory limits or other issues. Since it worked for the buildhost, I
suspect it's not a bug in the vlfeat package. Let me know if this
remains mysterious, and I'll ask for porterbox access and look into it
myself.

dima

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Bug#741073: gnuplot: Default 'apt-get install gnuplot' installs a non-x11 version

[Dima Kogan]

Package: gnuplot
Version: 4.7~2-4
Severity: normal
Hi.

This isn't strictly a bug, but a request. Currently the gnuplot
package is

  Depends: gnuplot-nox | gnuplot-x11 | gnuplot-qt

Thus when a user says apt-get install gnuplot, they get a gnuplot with
no support for interactive, graphical output. This is surely a safe
option, but it's not what most users want. I'm the author of a gnuplot
frontend (feedgnuplot), and at least 3 different people sent me bug
reports that were due to them accidentally installing a gnuplot without
graphical output.

This problem is exacerbated by gnuplot reporting no error messages at
all when trying to make plots with gnuplot-nox without setting up a
terminal first (another bug report coming for this).

I propose that gnuplot-nox be moved to the end of the dependency list,
since wanting this package is an exceptional case, not the normal one.

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Bug#741074: gnuplot-nox: By default no plots (or error messages) are generated

[Dima Kogan]

Package: gnuplot-nox
Version: 4.6.5-1
Severity: normal

Hi.

When using gnuplot-nox to make plots WITHOUT setting up a terminal,
gnuplot starts up with the unknown terminal. Any plot command then
results in no output AND no error messages. Example:

  dima@shorty:~$ dpkg -l gnuplot-nox
  Desired=Unknown/Install/Remove/Purge/Hold
  | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
  |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
  ||/ Name   Version  Architecture Description
  
+++-==---==
  ii  gnuplot-nox4.6.5-1  amd64Command-line 
driven interactive plotting program. 

  dima@shorty:~$ ls -l ~/.gnuplot
  ls: cannot access /home/dima/.gnuplot: No such file or directory

  dima@shorty:~$ gnuplot
  
  G N U P L O T
  Version 4.6 patchlevel 5last modified February 2014
  Build System: Linux x86_64
  
  Copyright (C) 1986-1993, 1998, 2004, 2007-2014
  Thomas Williams, Colin Kelley and many others
  
  gnuplot home: http://www.gnuplot.info
  faq, bugs, etc:   type help FAQ
  immediate help:   type help  (plot window: hit 'h')
  
  Terminal type set to 'unknown'
  gnuplot plot x
  gnuplot ^D


So no plot was generated, and no error message came through either. This
is a highly non-obvious failure, especially when using gnuplot
indirectly (with feedgnuplot, say). I think gnuplot should produce an
error message if trying to plot with an 'unknown' terminal, and I'll
suggest that upstream. Until then, I propose to set a default terminal
in

 /usr/share/gnuplot/gnuplot/4.6/gnuplotrc

so that we don't come up with the 'unknown' terminal. I suggest the
'dumb' terminal. This likely isn't what the user wants (although maybe
it IS, since they installed 'gnuplot-nox'), but it would be a highly
obvious behavior.

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Bug#741074: gnuplot-nox: By default no plots (or error messages) are generated

[Dima Kogan]

I sent a patch upstream:

 https://sourceforge.net/p/gnuplot/patches/660/

It would be great if the Debian package take this patch or change the
default terminal for gnuplot-nox, as I mentioned earlier.

dima

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