Debian Bug report logs - #598227
plplot is only buildable with the libhdf5-serial-dev package

Toggle useless messages

Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Matthias Klose <doko@ubuntu.com>

To: Debian Bug Tracking System <submit@bugs.debian.org>

Subject: plplot is only buildable with the libhdf5-serial-dev package

Date: Mon, 27 Sep 2010 19:12:14 +0200

Package: plplot
Version: 5.9.5-4
Severity: important
Tag: patch
User: ubuntu-devel@lists.ubuntu.com
Usertags: origin-ubuntu maverick ubuntu-patch

Found this while looking at build failures in maverick, but afaics it's the same 
with the plplot package in testing/unstable:

I did see:
[ 16%] Generating plplot_octave.oct
cd /scratch/packages/tmp/plplot-5.9.5/debian/build_tmp/bindings/octave && 
/usr/bin/mkoctfile 
/scratch/packages/tmp/plplot-5.9.5/debian/build_tmp/bindings/octave/plplot_octave.cc 
-I/scratch/packages/tmp/plplot-5.9.5/debian/build_tmp/bindings/octave 
-I/scratch/packages/tmp/plplot-5.9.5/bindings/octave 
-I/scratch/packages/tmp/plplot-5.9.5/include --strip 
-L/scratch/packages/tmp/plplot-5.9.5/debian/build_tmp/src -lplplotd
In file included from /usr/include/hdf5.h:24,
                 from /usr/include/octave-3.2.4/octave/oct-hdf5.h:32,
                 from /usr/include/octave-3.2.4/octave/ov.h:43,
                 from /usr/include/octave-3.2.4/octave/oct-obj.h:35,
                 from /usr/include/octave-3.2.4/octave/ov-fcn.h:33,
                 from /usr/include/octave-3.2.4/octave/ov-builtin.h:29,
                 from /usr/include/octave-3.2.4/octave/defun-int.h:29,
                 from /usr/include/octave-3.2.4/octave/defun-dld.h:31,
                 from /usr/include/octave-3.2.4/octave/oct.h:36,
                 from 
/scratch/packages/tmp/plplot-5.9.5/debian/build_tmp/bindings/octave/plplot_octave.cc:11:
/usr/include/H5public.h:57: fatal error: mpi.h: No such file or directory
compilation terminated.
make[3]: *** [bindings/octave/plplot_octave.oct] Error 1

plplot b-d's on octave3.2-headers, which depend on

libhdf5-serial-dev (>= 1.8.4) | libhdf5-lam-dev (>= 1.8.4) | libhdf5-mpich-dev 
(>= 1.8.4) | libhdf5-openmpi-dev (>= 1.8.4)

but plplot is only buildable with the -serial variant:

$ fgrep PARALLEL ./debian/libhdf5-serial-dev/usr/include/H5pubconf.h 
./debian/libhdf5-openmpi-dev/usr/include/H5pubconf.h 
./debian/libhdf5-lam-dev/usr/include/H5pubconf.h 
./debian/libhdf5-mpich-dev/usr/include/H5pubconf.h
./debian/libhdf5-serial-dev/usr/include/H5pubconf.h:/* #undef H5_HAVE_PARALLEL */
./debian/libhdf5-openmpi-dev/usr/include/H5pubconf.h:#define H5_HAVE_PARALLEL 1
./debian/libhdf5-lam-dev/usr/include/H5pubconf.h:#define H5_HAVE_PARALLEL 1
./debian/libhdf5-mpich-dev/usr/include/H5pubconf.h:#define H5_HAVE_PARALLEL 1

so plplot must directly b-d on libhdf5-serial-dev.

Message #14 received at 598227@bugs.debian.org (full text, mbox, reply):

From: Andrew Ross <andrewross@users.sourceforge.net>

To: 598227@bugs.debian.org

Subject: plplot is only buildable with the libhdf5-serial-dev package

Date: Tue, 28 Sep 2010 10:47:22 +0100

Having investigated further, it looks like the cause of the problem is
that oct.h includes hdf.h, which eventually includes mpi.h if the mpi 
version of the hdf libraries is installed. Unfortunately this seems to be
installed in /usr/include/mpi/ , so unless I build with an explicit
-I/usr/include/mpi option, then the build will fail. 

It seems crazy to me that I should have to do this just to use the octave
headers. The best solution would be for /usr/include/H5public.h to include
mpi/mpi.h, and then things would work irrespective of whether the serial or
mpi version of the hdf libraries was installed.

Andrew

Message #19 received at 598227@bugs.debian.org (full text, mbox, reply):

From: Andrew Ross <andrewross@users.sourceforge.net>

To: 598227@bugs.debian.org

Subject: plplot is only buildable with the libhdf5-serial-dev package

Date: Tue, 28 Sep 2010 11:03:02 +0100

I've done some more digging and just replacing mpi.h with mpi/mpi.h doesn't
work as other files in /usr/include/mpi are also included further on. Perhaps 
the best solution is to ensure that mkoctfile automatically adds
/usr/include/mpi into the include path where required. This will then just
work for all users of the octave headers (assuming they use mkoctfile -
which is the recommended way of building octave extensions). 

Andrew

-- 
 Dr Andrew Ross                 Email: A.N.Ross@leeds.ac.uk  
 Inst. for Climate and Atmospheric Science, Sch. of Earth and Environment, 
 University of Leeds, Leeds, LS2 9JT, UK.  Tel/Fax: +44 113 343 7590/5259 

Message #24 received at 598227@bugs.debian.org (full text, mbox, reply):

From: Thomas Weber <tweber@debian.org>

To: Andrew Ross <andrewross@users.sourceforge.net>, 598227@bugs.debian.org

Subject: Re: [Pkg-octave-devel] Bug#598227: plplot is only buildable with the libhdf5-serial-dev package

Date: Sun, 3 Oct 2010 11:42:43 +0200

Hi Andrew, 
On Tue, Sep 28, 2010 at 11:03:02AM +0100, Andrew Ross wrote:
> 
> I've done some more digging and just replacing mpi.h with mpi/mpi.h doesn't
> work as other files in /usr/include/mpi are also included further on. Perhaps 
> the best solution is to ensure that mkoctfile automatically adds
> /usr/include/mpi into the include path where required. This will then just
> work for all users of the octave headers (assuming they use mkoctfile -
> which is the recommended way of building octave extensions). 

I've asked on pkg-grass-devel (maintainers of hdf5) how to best proceed
here. I'm reluctant to change mkoctfile, maybe there's a better way.

Thanks
	Thomas

Message #29 received at 598227@bugs.debian.org (full text, mbox, reply):

From: Thomas Weber <tweber@debian.org>

To: Debian Release <debian-release@lists.debian.org>

Cc: 598227@bugs.debian.org

Subject: Freeze exception for Octave

Date: Sun, 24 Oct 2010 23:43:11 +0200

[Message part 1 (text/plain, inline)]

Hi, 

in order to fix #598227 (http://bugs.debian.org/598227), I would like to
upload octave with the attached patch (it adds /usr/include/mpi to the
include path used by mkoctfile, the script used for generating 'addons'
for Octave). It shouldn't have any influence on other packages.

Post-Squeeze, Octave will switch to only use the serial version of hdf5,
but I'm reluctant to make this change now.

Are you guys okay with the patch?

Thanks
	Thomas

[include_mpi_headers (text/plain, attachment)]

Message #34 received at 598227@bugs.debian.org (full text, mbox, reply):

From: Mehdi Dogguy <mehdi@dogguy.org>

To: Debian Release <debian-release@lists.debian.org>, 598227@bugs.debian.org

Subject: Re: Freeze exception for Octave

Date: Mon, 25 Oct 2010 16:24:24 +0200

On 10/24/2010 11:43 PM, Thomas Weber wrote:
> Hi, 
> 
> in order to fix #598227 (http://bugs.debian.org/598227), I would like to
> upload octave with the attached patch (it adds /usr/include/mpi to the
> include path used by mkoctfile, the script used for generating 'addons'
> for Octave). It shouldn't have any influence on other packages.
> 
> Post-Squeeze, Octave will switch to only use the serial version of hdf5,
> but I'm reluctant to make this change now.
> 
> Are you guys okay with the patch?
> 

Yes, please go ahead with the upload.

> Thanks
> 	Thomas

-- 
Mehdi Dogguy مهدي الدڤي
http://dogguy.org/

Message #41 received at 598227-close@bugs.debian.org (full text, mbox, reply):

From: Thomas Weber <tweber@debian.org>

To: 598227-close@bugs.debian.org

Subject: Bug#598227: fixed in octave3.2 3.2.4-8

Date: Mon, 25 Oct 2010 22:18:18 +0000

Source: octave3.2
Source-Version: 3.2.4-8

We believe that the bug you reported is fixed in the latest version of
octave3.2, which is due to be installed in the Debian FTP archive:

octave3.2-common_3.2.4-8_all.deb
  to main/o/octave3.2/octave3.2-common_3.2.4-8_all.deb
octave3.2-dbg_3.2.4-8_amd64.deb
  to main/o/octave3.2/octave3.2-dbg_3.2.4-8_amd64.deb
octave3.2-doc_3.2.4-8_all.deb
  to main/o/octave3.2/octave3.2-doc_3.2.4-8_all.deb
octave3.2-emacsen_3.2.4-8_all.deb
  to main/o/octave3.2/octave3.2-emacsen_3.2.4-8_all.deb
octave3.2-headers_3.2.4-8_amd64.deb
  to main/o/octave3.2/octave3.2-headers_3.2.4-8_amd64.deb
octave3.2-htmldoc_3.2.4-8_all.deb
  to main/o/octave3.2/octave3.2-htmldoc_3.2.4-8_all.deb
octave3.2-info_3.2.4-8_all.deb
  to main/o/octave3.2/octave3.2-info_3.2.4-8_all.deb
octave3.2_3.2.4-8.diff.gz
  to main/o/octave3.2/octave3.2_3.2.4-8.diff.gz
octave3.2_3.2.4-8.dsc
  to main/o/octave3.2/octave3.2_3.2.4-8.dsc
octave3.2_3.2.4-8_amd64.deb
  to main/o/octave3.2/octave3.2_3.2.4-8_amd64.deb



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

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 598227@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Thomas Weber <tweber@debian.org> (supplier of updated octave3.2 package)

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


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Format: 1.8
Date: Mon, 25 Oct 2010 21:44:40 +0200
Source: octave3.2
Binary: octave3.2 octave3.2-doc octave3.2-htmldoc octave3.2-headers octave3.2-emacsen octave3.2-info octave3.2-dbg octave3.2-common
Architecture: source amd64 all
Version: 3.2.4-8
Distribution: unstable
Urgency: low
Maintainer: Debian Octave Group <pkg-octave-devel@lists.alioth.debian.org>
Changed-By: Thomas Weber <tweber@debian.org>
Description: 
 octave3.2  - GNU Octave language for numerical computations (3.2 branch)
 octave3.2-common - architecture-independent files for octave3.2
 octave3.2-dbg - Debug symbols for octave3.2
 octave3.2-doc - PDF documentation on the GNU Octave language (3.2 branch)
 octave3.2-emacsen - Emacs support for the GNU Octave language (3.2 branch)
 octave3.2-headers - header files for the GNU Octave language (3.2 branch)
 octave3.2-htmldoc - HTML documentation on the GNU Octave language (3.2 branch)
 octave3.2-info - GNU Info documentation on the GNU Octave language (3.2 branch)
Closes: 598227
Changes: 
 octave3.2 (3.2.4-8) unstable; urgency=low
 .
   * New patch: include_mpi_headers, includes /usr/include/mpi by default when
     using mkoctfile (closes: #598227)
Checksums-Sha1: 
 460df7284f174fadd9948d6bd7e473b72f73568c 1984 octave3.2_3.2.4-8.dsc
 a9105bae541a7023367d1eab81e95948fe95bd78 67461 octave3.2_3.2.4-8.diff.gz
 033009f88891940d26057049b73fe5fd1ee4f24b 10157024 octave3.2_3.2.4-8_amd64.deb
 b05c1439fdbfe2cc2898ef1d5dae91ec4fe0c114 536198 octave3.2-headers_3.2.4-8_amd64.deb
 2caa48fccd560368a59c2f4edb572ce0305199ec 64657382 octave3.2-dbg_3.2.4-8_amd64.deb
 b8ed9412cd47889111d608b8203f9a20af0a2cdf 3203986 octave3.2-doc_3.2.4-8_all.deb
 e839b3c8995b0cbacdf769bb620afdee47a65888 1036950 octave3.2-htmldoc_3.2.4-8_all.deb
 e12e947cf08af13ce352ab62176aab8aa9b0f012 109834 octave3.2-emacsen_3.2.4-8_all.deb
 7549aec84140e00e04f4a778a1d60c03bf9e6f85 561212 octave3.2-info_3.2.4-8_all.deb
 f809049732eb214da1e793fea35e6deeb8726f59 672740 octave3.2-common_3.2.4-8_all.deb
Checksums-Sha256: 
 ed32f05fed0e2c206bd559ebcbe9c62fec91ad20e3a447179c0d67b870234126 1984 octave3.2_3.2.4-8.dsc
 b96ad2a15fb6034a4fffeecb2f7ea181227b59b8c6ec44a6fb7dbaabe010af1c 67461 octave3.2_3.2.4-8.diff.gz
 613a25644485b1831b9ef3e7ab8980d79a4c63d53a324d4a59010db01e26e2a9 10157024 octave3.2_3.2.4-8_amd64.deb
 6c1d5f2970b4e942ea00cb2d2ced3bc2ee5a6df6ffc0f4245279a1e1fc25bd2a 536198 octave3.2-headers_3.2.4-8_amd64.deb
 f8334aabe39393ebc19d315fbf0e4f9d68470a29c836cb9723b1580a83e9215d 64657382 octave3.2-dbg_3.2.4-8_amd64.deb
 a7186afeee07dd605ace69d00cb98e29d9030a4a20fcd769c19bbc864b8ef374 3203986 octave3.2-doc_3.2.4-8_all.deb
 c2c62ceeee10bf5895993290a526a72f7445fdcf4466926836fab208c4e787e9 1036950 octave3.2-htmldoc_3.2.4-8_all.deb
 562c16255fbf6bbe83a3131a678c4287f1d0c3f51b94feacaf0ebc8bd568c581 109834 octave3.2-emacsen_3.2.4-8_all.deb
 558f46ab147abd8335bf9feec6f18d123f5307cb13c246efb29cc0de680dce5e 561212 octave3.2-info_3.2.4-8_all.deb
 0c79031ac04cbe129ed9134c6a9176b3e9cdf7ce8d4136a29019a687705b0ca6 672740 octave3.2-common_3.2.4-8_all.deb
Files: 
 bf9aa4e33e02002464d158b905cc5399 1984 math optional octave3.2_3.2.4-8.dsc
 ea53f9e48a2653f5a2520b208f89f3ba 67461 math optional octave3.2_3.2.4-8.diff.gz
 f6bff1b56b6b94dd307201675569a0f1 10157024 math optional octave3.2_3.2.4-8_amd64.deb
 a09f3642ec2d7474b6334ade71b81da0 536198 math optional octave3.2-headers_3.2.4-8_amd64.deb
 1417dbdffcaeed61e114498aaef2d268 64657382 debug extra octave3.2-dbg_3.2.4-8_amd64.deb
 00ef9a6888c2af149ff5ad295c280734 3203986 doc optional octave3.2-doc_3.2.4-8_all.deb
 6f7315649beb4770d0afe39e6a8d6b04 1036950 doc optional octave3.2-htmldoc_3.2.4-8_all.deb
 2cf9ee6babab3dd1d707c2089435f9fb 109834 math optional octave3.2-emacsen_3.2.4-8_all.deb
 1b6389cf99cc37559532d197e689b0a1 561212 math optional octave3.2-info_3.2.4-8_all.deb
 170295fcbc7026e61b7a555949573aa4 672740 devel extra octave3.2-common_3.2.4-8_all.deb

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.9 (GNU/Linux)

iEYEARECAAYFAkzF/DMACgkQPqD4a3lPnXyIdACfUiMzpjrz+JG4muQBsu33t6xe
kOIAniJYLg9cTSjpuF4qBTvrt3R0tUxy
=Kp5M
-----END PGP SIGNATURE-----

Send a report that this bug log contains spam.