Re: python-pbcore 1.2.2

[Andreas Tille]

Hi,

On Tue, Aug 11, 2015 at 07:45:02PM -0700, Afif Elghraoui wrote:
> Hi, team,
> I have prepared an update to this package, but had to drop the
> (apparently nonfunctional) Python 3 version that I created the first
> time. Python 3 is not supported upstream yet, but is planned in the
> future [1]. The package has to pass NEW again. Would someone please upload?

Upload to unstable or experimental?  (If it should stay in experimental
I would not mind too much about some broken functionality of Python3.)
I'm asking since you left UNRELEASED (which is fine) but last upload was
to experimental.

Kind regards

  Andreas.

-- 
http://fam-tille.de


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Re: python-pbcore 1.2.2

[Afif Elghraoui]

On الأربعاء 12 آب 2015 00:37, Andreas Tille wrote:
> Hi,
> 
> On Tue, Aug 11, 2015 at 07:45:02PM -0700, Afif Elghraoui wrote:
>> Hi, team,
>> I have prepared an update to this package, but had to drop the
>> (apparently nonfunctional) Python 3 version that I created the first
>> time. Python 3 is not supported upstream yet, but is planned in the
>> future [1]. The package has to pass NEW again. Would someone please upload?
> 
> Upload to unstable or experimental?  (If it should stay in experimental
> I would not mind too much about some broken functionality of Python3.)
> I'm asking since you left UNRELEASED (which is fine) but last upload was
> to experimental.
> 

Oh, sorry-- unstable. The Python 3 package was failing almost all the
tests. The porting is non-trivial and it doesn't appear upstream is
willing to cooperate on this yet.

Many thanks and regards

Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name


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DebianMed policy error

[olivier sallou]

Hi,
there is an error in DebianMed policy page [0]:

*svn-buildpackage* --svn-tag-only
=> --svn-only-tag

[0] http://debian-med.alioth.debian.org/docs/policy.html

Olivier

Re: DebianMed policy error

[Charles Plessy]

Le Wed, Aug 12, 2015 at 09:12:34AM +, olivier sallou a écrit :
> 
> there is an error in DebianMed policy page [0]:
> 
> *svn-buildpackage* --svn-tag-only
> => --svn-only-tag

Bonjour Olivier,

I just realised that svn-buildpackage accepts both (according to its manpage).

Have a nice day,

Charles

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


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Re: DebianMed policy error

[Sascha Steinbiss]

Hi,

Btw, in the same paragraph, I think it should additionally be
'--svn-noautodch' instead of '--svn-no-autodch':

[vagrant@debian-8:~] $ svn-buildpackage --help | grep autodch
  --svn-noautodch  Don't add a new Debian changelog entry when done

Cheers
Sascha

On 12/08/2015 10:12, olivier sallou wrote:
> Hi,
> there is an error in DebianMed policy page [0]:
> 
> *svn-buildpackage* |--svn-tag-only|
> |=> --svn-only-tag|
> |
> |
> |[0] http://debian-med.alioth.debian.org/docs/policy.html|
> |
> |
> |Olivier|


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


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Re: DebianMed policy error

[Andreas Tille]

Hi,

if anybody spots an error - the policy is in SVN and can be fixed by
anybody.  You can use

make publish

to push it online easily.

Kind regards

  Andreas.

On Wed, Aug 12, 2015 at 10:25:55AM +0100, Sascha Steinbiss wrote:
> Hi,
> 
> Btw, in the same paragraph, I think it should additionally be
> '--svn-noautodch' instead of '--svn-no-autodch':
> 
> [vagrant@debian-8:~] $ svn-buildpackage --help | grep autodch
>   --svn-noautodch  Don't add a new Debian changelog entry when done
> 
> Cheers
> Sascha
> 
> On 12/08/2015 10:12, olivier sallou wrote:
> > Hi,
> > there is an error in DebianMed policy page [0]:
> > 
> > *svn-buildpackage* |--svn-tag-only|
> > |=> --svn-only-tag|
> > |
> > |
> > |[0] http://debian-med.alioth.debian.org/docs/policy.html|
> > |
> > |
> > |Olivier|
> 
> 
> -- 
>  The Wellcome Trust Sanger Institute is operated by Genome Research 
>  Limited, a charity registered in England with number 1021457 and a 
>  company registered in England with number 2742969, whose registered 
>  office is 215 Euston Road, London, NW1 2BE. 
> 
> 
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> 
> 

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Re: Help needed to update to latest fastqc

[Tim Booth]

Hi Andreas and Olivier,

I'm going to have a crack at the FastQC update.  I've been poking at the
HDF5 packages and here are my conclusions so far:

---

We have 2 Free Java libraries for HDF5:

1) The "NCSA" lib distributed by hdfgroup.org with classes in namespace
ncsa.hdf.hdf5lib, packaged on Debian as libjhdf5-java.

2) The "CISD" aka. "SIS" lib distributed by ethz.ch with classes in the
namespace ch.systemsx, not currently packaged on Debian.

The SIS library forks some Java code from the ncsa.hdf namespace, and
also needs to link against the NCSA native library (via JNI) at runtime.

So, trying to package sis-jhdf5:

wget
'https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.1-r33502.zip?version=1&modificationDate=1424599261225&api=v2'
# The source is in a zip within the zip...
unzip sis-*
mkdir sis-jhdf5-14.12.1
cd !$
unzip ../sis-jhdf5/src/sis-jhdf5-src.zip

For compilation to succeed, we also need sis-base, not to be confused
with the entirely separate project at sis.apache.org!

wget
http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/sis-base/sis-base-src.zip

The code also depends on their own args4j library, but only for the CLI
under ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java which we can
simply leave out just now.

So - can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and
compile it against the existing classes in /usr/share/java/jhdf5.jar?
My conclusion is not, because...

The version of ncsa/hdf/hdf5lib/exceptions/HDF5Exception.java supplied
with the sis-jhdf5 code subclasses RuntimeException but the version in
libhdf5-java does not.  The result is that the code here does not need
to declare the exceptions being thrown, and thus simply ignores them
all.  One can go through and add all "throws" declarations (there are a
_lot_ of them!!), but then any client code using the library will also
break unless it is likewise patched or the code is modified to handle
the exceptions internally. I think we'd best just admit defeat here and
use the code supplied with sis-jhdf5.

So, I'm going to try rolling two new packages, and see if that allows me
to compile the latest FastQC:

libsis-base-java (should be simple)
libsis-jhdf5-java (depends on libsis-base-java + existing libjhdf5-jni)

I'll report back on progress and commit to SVN as usual.  Let me know if
you think I'm missing something.

Cheers,

TIM


On Thu, 2015-06-25 at 09:37 +0200, Andreas Tille wrote:
> Hi Olivier,
> 
> any news about this hdf5lib packaging?
> 
> Kind regards
> 
>  Andreas.
> 
> On Tue, May 05, 2015 at 09:25:23AM +0200, Olivier Sallou wrote:
> > 
> > 
> > On 05/04/2015 10:52 PM, Andreas Tille wrote:
> > > Hi Olivier,
> > >
> > > On Mon, May 04, 2015 at 06:41:10PM +0200, Olivier Sallou wrote:
> > >> File fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java imports
> > >> HDFS5Factory from ch.systemsx.cisd.hdf5
> > >>
> > >> but jhdf5.jar only contains files like:  ncsa/hdf/hdf5lib/... and no
> > >> HDF5Factory
> > >>
> > >> this jhdf5 is not the correctl lib (or an other one is needed).
> > > I guess its this one:
> > >
> > > 
> > > https://svncisd.ethz.ch/doc/hdf5/hdf5-8.10/ch/systemsx/cisd/hdf5/package-summary.html
> > seems that original code source is the same
> > (https://svncisd.ethz.ch/repos/cisd/jhdf5/trunk/source/java/)
> > (/ncsa/...) but that /ch/...  has not been included for a reason
> > >  
> > >> In addition, in debian/patches/build.xml is missing commons-math3.jar to
> > >> be added in pathelement for classpath.
> > >>
> > >> for duplicate classes, I don't yet, but hdf5 first need to be resolved.
> > > If I do not hear from you I'll try the URL above tomorrow (if nobody
> > > else might beat me which would for sure welcome as always).
> > >
> > > Kind regards
> > >
> > >   Andreas.
> > >
> > 
> > -- 
> > Olivier Sallou
> > IRISA / University of Rennes 1
> > Campus de Beaulieu, 35000 RENNES - FRANCE
> > Tel: 02.99.84.71.95
> > 
> > gpg key id: 4096R/326D8438  (keyring.debian.org)
> > Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438
> > 
> > 
> > -- 
> > To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
> > with a subject of "unsubscribe". Trouble? Contact 
> > listmas...@lists.debian.org
> > Archive: https://lists.debian.org/55487063.1090...@irisa.fr
> > 
> > 
> 
> -- 
> http://fam-tille.de
> 
> 

-- 
Nothing is inherently mysterious - nothing that actually exists, that
is.  If I am ignorant about a phenomenon, that is a fact about my state
of mind, not a fact about the phenomenon; to worship a phenomenon
because it seems so wonderfully mysterious, is to worship your own
ignorance.

  - Eliezer Yudkowsky


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Re: Help needed to update to latest fastqc

[Andreas Tille]

Hi Tim,

from my *very* naive point of view your considerations make sense.
Olivier might have some more educated opinion (and perhaps some code?).

I'll be available vor sponsering as usual.

Thanks for your work on this

 Andreas.

On Wed, Aug 12, 2015 at 11:44:19AM +0100, Tim Booth wrote:
> Hi Andreas and Olivier,
> 
> I'm going to have a crack at the FastQC update.  I've been poking at the
> HDF5 packages and here are my conclusions so far:
> 
> ---
> 
> We have 2 Free Java libraries for HDF5:
> 
> 1) The "NCSA" lib distributed by hdfgroup.org with classes in namespace
> ncsa.hdf.hdf5lib, packaged on Debian as libjhdf5-java.
> 
> 2) The "CISD" aka. "SIS" lib distributed by ethz.ch with classes in the
> namespace ch.systemsx, not currently packaged on Debian.
> 
> The SIS library forks some Java code from the ncsa.hdf namespace, and
> also needs to link against the NCSA native library (via JNI) at runtime.
> 
> So, trying to package sis-jhdf5:
> 
> wget
> 'https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.1-r33502.zip?version=1&modificationDate=1424599261225&api=v2'
> # The source is in a zip within the zip...
> unzip sis-*
> mkdir sis-jhdf5-14.12.1
> cd !$
> unzip ../sis-jhdf5/src/sis-jhdf5-src.zip
> 
> For compilation to succeed, we also need sis-base, not to be confused
> with the entirely separate project at sis.apache.org!
> 
> wget
> http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/sis-base/sis-base-src.zip
> 
> The code also depends on their own args4j library, but only for the CLI
> under ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java which we can
> simply leave out just now.
> 
> So - can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and
> compile it against the existing classes in /usr/share/java/jhdf5.jar?
> My conclusion is not, because...
> 
> The version of ncsa/hdf/hdf5lib/exceptions/HDF5Exception.java supplied
> with the sis-jhdf5 code subclasses RuntimeException but the version in
> libhdf5-java does not.  The result is that the code here does not need
> to declare the exceptions being thrown, and thus simply ignores them
> all.  One can go through and add all "throws" declarations (there are a
> _lot_ of them!!), but then any client code using the library will also
> break unless it is likewise patched or the code is modified to handle
> the exceptions internally. I think we'd best just admit defeat here and
> use the code supplied with sis-jhdf5.
> 
> So, I'm going to try rolling two new packages, and see if that allows me
> to compile the latest FastQC:
> 
> libsis-base-java (should be simple)
> libsis-jhdf5-java (depends on libsis-base-java + existing libjhdf5-jni)
> 
> I'll report back on progress and commit to SVN as usual.  Let me know if
> you think I'm missing something.
> 
> Cheers,
> 
> TIM
> 
> 
> On Thu, 2015-06-25 at 09:37 +0200, Andreas Tille wrote:
> > Hi Olivier,
> > 
> > any news about this hdf5lib packaging?
> > 
> > Kind regards
> > 
> >  Andreas.
> > 
> > On Tue, May 05, 2015 at 09:25:23AM +0200, Olivier Sallou wrote:
> > > 
> > > 
> > > On 05/04/2015 10:52 PM, Andreas Tille wrote:
> > > > Hi Olivier,
> > > >
> > > > On Mon, May 04, 2015 at 06:41:10PM +0200, Olivier Sallou wrote:
> > > >> File fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java imports
> > > >> HDFS5Factory from ch.systemsx.cisd.hdf5
> > > >>
> > > >> but jhdf5.jar only contains files like:  ncsa/hdf/hdf5lib/... and no
> > > >> HDF5Factory
> > > >>
> > > >> this jhdf5 is not the correctl lib (or an other one is needed).
> > > > I guess its this one:
> > > >
> > > > 
> > > > https://svncisd.ethz.ch/doc/hdf5/hdf5-8.10/ch/systemsx/cisd/hdf5/package-summary.html
> > > seems that original code source is the same
> > > (https://svncisd.ethz.ch/repos/cisd/jhdf5/trunk/source/java/)
> > > (/ncsa/...) but that /ch/...  has not been included for a reason
> > > >  
> > > >> In addition, in debian/patches/build.xml is missing commons-math3.jar 
> > > >> to
> > > >> be added in pathelement for classpath.
> > > >>
> > > >> for duplicate classes, I don't yet, but hdf5 first need to be resolved.
> > > > If I do not hear from you I'll try the URL above tomorrow (if nobody
> > > > else might beat me which would for sure welcome as always).
> > > >
> > > > Kind regards
> > > >
> > > >   Andreas.
> > > >
> > > 
> > > -- 
> > > Olivier Sallou
> > > IRISA / University of Rennes 1
> > > Campus de Beaulieu, 35000 RENNES - FRANCE
> > > Tel: 02.99.84.71.95
> > > 
> > > gpg key id: 4096R/326D8438  (keyring.debian.org)
> > > Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438
> > > 
> > > 
> > > -- 
> > > To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
> > > with a subject of "unsubscribe". Trouble? Contact 
> > > listmas...@lists.debian.org
> > > Archive: https://lists.debian.org/55487063.1090...@irisa.fr
> > > 
> > > 
> > 
> > -- 
> > http://fam-tille.de
> > 
> > 
> 
> -- 
> Nothing is inherently mysterious - nothing that actually exists, that

Re: Help needed to update to latest fastqc

[Tim Booth]

Hi,

After a fair amount of struggling I conclude that I do not have all the
code required to build this thing from source.

The distribution of JHDF5 from
https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=26609113
contains some Java source code and a bunch of pre-compiled JNI shared
libs, eg.:

sis-jhdf5/lib/native/jhdf5/amd64-Linux/libjhdf5.so

The source for this file is not to be found anywhere that I can see it.
One might assume (and the FAQ implies) that the file is equivalent
to /usr/lib/jni/libjhdf5.so provided by the exiting package libjhdf5-jni
but it isn't!  Inspecting it with readelf shows it is full of symbols in
the ETH SIS namespace:

tbooth@balisaur[sis-jhdf5] readelf -sW 
./sis-jhdf5/lib/native/jhdf5/amd64-Linux/libjhdf5.so | grep ch_systemsx | head
19: 00039a4058 FUNCGLOBAL DEFAULT   10 
Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Scopy
31: 0002e930   181 FUNCGLOBAL DEFAULT   10 
Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dchdir_1ext
35: 0003b590   918 FUNCGLOBAL DEFAULT   10 
Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sget_1select_1bounds
40: 000387f045 FUNCGLOBAL DEFAULT   10 
Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pcreate_1xfer_1abort
41: 0003882066 FUNCGLOBAL DEFAULT   10 
Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1char_1encoding
46: 00034500   203 FUNCGLOBAL DEFAULT   10 
Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Oopen
47: 00034ae0   363 FUNCGLOBAL DEFAULT   10 
Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1version
52: 0003521066 FUNCGLOBAL DEFAULT   10 
Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1layout
65: 0003c560   126 FUNCGLOBAL DEFAULT   10 
Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1member_1name
68: 00032da058 FUNCGLOBAL DEFAULT   10 
Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Idec_1ref
...and many more...

So, this .so file is definitely specific to this library.  It seems to
be a superset of a fork of the upstream NCSA code.  The only contact
details I can find for the library are for Dr. Bernd Rinn who is the
head of the whole division, but I shall contact him personally and see
if he can pass the query on.

If Bernd can't help, then unless I've missed a trick we will have to
consider that this library and anything that depends on it (eg FastQC)
are not fully open source :-(

Cheers,

TIM

On Wed, 2015-08-12 at 15:00 +0200, Andreas Tille wrote:
> Hi Tim,
> 
> from my *very* naive point of view your considerations make sense.
> Olivier might have some more educated opinion (and perhaps some code?).
> 
> I'll be available vor sponsering as usual.
> 
> Thanks for your work on this
> 
>  Andreas.
> 
> On Wed, Aug 12, 2015 at 11:44:19AM +0100, Tim Booth wrote:
> > Hi Andreas and Olivier,
> > 
> > I'm going to have a crack at the FastQC update.  I've been poking at the
> > HDF5 packages and here are my conclusions so far:
> > 
> > ---
> > 
> > We have 2 Free Java libraries for HDF5:
> > 
> > 1) The "NCSA" lib distributed by hdfgroup.org with classes in namespace
> > ncsa.hdf.hdf5lib, packaged on Debian as libjhdf5-java.
> > 
> > 2) The "CISD" aka. "SIS" lib distributed by ethz.ch with classes in the
> > namespace ch.systemsx, not currently packaged on Debian.
> > 
> > The SIS library forks some Java code from the ncsa.hdf namespace, and
> > also needs to link against the NCSA native library (via JNI) at runtime.
> > 
> > So, trying to package sis-jhdf5:
> > 
> > wget
> > 'https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.1-r33502.zip?version=1&modificationDate=1424599261225&api=v2'
> > # The source is in a zip within the zip...
> > unzip sis-*
> > mkdir sis-jhdf5-14.12.1
> > cd !$
> > unzip ../sis-jhdf5/src/sis-jhdf5-src.zip
> > 
> > For compilation to succeed, we also need sis-base, not to be confused
> > with the entirely separate project at sis.apache.org!
> > 
> > wget
> > http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/sis-base/sis-base-src.zip
> > 
> > The code also depends on their own args4j library, but only for the CLI
> > under ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java which we can
> > simply leave out just now.
> > 
> > So - can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and
> > compile it against the existing classes in /usr/share/java/jhdf5.jar?
> > My conclusion is not, because...
> > 
> > The version of ncsa/hdf/hdf5lib/exceptions/HDF5Exception.java supplied
> > with the sis-jhdf5 code subclasses RuntimeException but the version in
> > libhdf5-java does not.  The result is that the code here does not need
> > to declare the exceptions being thrown, and thus simply ignores them
> > all.  One can go through and add all "throws" declarations (there are a
> > _lot_ of them!!), but then any client code using the library will also
> > break unless it is likewise patched or the code is modified to handle
> > the exceptions internally. I think we'

Wgsim stays in samtools.

[Charles Plessy]

Hello everyone,

in conclusion, wgsim stays in samtools, where it will only get bug fixes, but
no further developments. 

https://github.com/samtools/samtools/issues/429#issuecomment-129412846

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

Please update from ITK v3 to v4 [Re: RM: insighttoolkit -- ROM; Obsoleted by insighttoolkit4]

[Steve M. Robbins]

Hi,

Previously on debian-med, I proposed that ITK v3 be dropped from the archive 
[1].  The only respondent agreed with that.  So I filed for removal [2] and 
received notice that several packages still depend on ITK v3 (e.g. on 
libinsighttoolkit3-dev).  Could those package maintainers update to v4, 
please?

Thanks,
-Steve

[1] https://lists.debian.org/debian-med/2015/08/msg00010.html
[2] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=795019


On August 12, 2015 11:54:07 AM you wrote:
> On Sunday, August 09, 2015 10:48:36 AM Steve M. Robbins wrote:
> > Package: ftp.debian.org
> > Severity: normal
> > 
> > The package is already scheduled for autoremoval due to GCC 5 issues.
> > But there is no need to wait: the code is several years old and will
> > not be maintained.  Successor package is insighttoolkit4.
> 
> Has rdepends that need updating.  Please remove the moreinfo tag once these
> are updated.
> 
> Checking reverse dependencies...
> # Broken Depends:
> camitk: libcamitk3
> fw4spl: fw4spl [amd64]
> ginkgocadx: ginkgocadx [amd64 armel armhf i386 mips mipsel powerpc ppc64el
> s390x]
> gofigure2: gofigure2 [amd64 armel armhf hurd-i386 i386 kfreebsd-amd64
> kfreebsd- i386 mips mipsel powerpc ppc64el s390x]
>libgofigure0 [amd64 armel armhf hurd-i386 i386 kfreebsd-amd64
> kfreebsd-i386 mips mipsel powerpc ppc64el s390x]
> igstk: libigstk4 [amd64 armel armhf hurd-i386 i386 kfreebsd-amd64 kfreebsd-
> i386 mips mipsel powerpc s390x]
>libigstk4-dev [amd64 armel armhf hurd-i386 i386 kfreebsd-amd64
> kfreebsd-i386 mips mipsel powerpc s390x]
> itksnap: itksnap [armel armhf hurd-i386 kfreebsd-amd64 kfreebsd-i386 mips
> mipsel powerpc ppc64el s390x]
> nifti2dicom: nifti2dicom [armel armhf hurd-i386 kfreebsd-amd64 kfreebsd-i386
> mips mipsel powerpc ppc64el s390x]
>  qnifti2dicom [armel armhf hurd-i386 kfreebsd-amd64
> kfreebsd-i386 mips mipsel powerpc ppc64el s390x]
> plastimatch: plastimatch [arm64 armel armhf kfreebsd-amd64 kfreebsd-i386
> mips mipsel powerpc ppc64el s390x]
> vmtk/non-free: libvmtk1.0
>python-vmtk
> 
> # Broken Build-Depends:
> camitk: libinsighttoolkit3-dev (>= 3.20)
> fw4spl: libinsighttoolkit3-dev
> ginkgocadx: libinsighttoolkit3-dev (>= 3.20.0)
> gofigure2: libinsighttoolkit3-dev (>= 3.20)
> igstk: libinsighttoolkit3-dev (>= 3.20)
> itksnap: libinsighttoolkit3-dev
> 
> Dependency problem found.


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Re: Please update from ITK v3 to v4 [Re: RM: insighttoolkit -- ROM; Obsoleted by insighttoolkit4]

[Dmitry Smirnov]

On Wednesday 12 August 2015 22:01:36 Steve M. Robbins wrote:
> Could those package maintainers update to v4, please?

First ITK-4 needs to be re-build for GCC-5 transition. At the moment
"ginkgocadx" FTBFS in "unstable" (but not in "testing") due to

libstdc++6 : Breaks: libinsighttoolkit4.7 (<= 4.7.2-2) but 4.7.2-2 is to be 
installed.

-- 
Best wishes,
 Dmitry Smirnov.


---

You have to start with the truth. The truth is the only way that we can
get anywhere. Because any decision-making that is based upon lies or
ignorance can't lead to a good conclusion.
-- Julian Assange, 2010


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Re: gcc-5 transition of GDCM

[michkapopoff]

> On August 5, 2015 03:29:30 PM Sébastien Jodogne wrote:
> 
>>> I will try hard to get the script into VCS tonight and then I will welcome
>>> help in testing the builds on dependent packages.
>> 
>> Great! Let me know when things are ready.
> 
> OK.  The gccxml package is updated with a wrapper around castxml (the real
> binary is renamed to gccxml.real).
> 
> Still working on testing build-deps with it.  Sadly, pygccxml fails :-(
> 
> -Steve
> 

Hi

I was told someone mentioned pygccxml here :)

I am the current maintainer of the project (https://github.com/gccxml/pygccxml 
).
During the last months I worked on the integration of CastXML in pygccxml and I 
am
almost done. Basically, there were around 80 unit tests failing, and I am down
to 10 failing tests. The core unit tests are running, and ITK already uses 
pygccxml
internally. So as long as one does not do fancy stuff, it should be ok.

I delayed the new release in the hope to be able to fix the remaining tests; 
but this
takes a lot of time (as I did not write pygccxml in the first place, I am 
discovering
the code). But I think there is some pressure to release a new version with 
basic
support so people can start using it. I even heard from 1 or 2 people which are 
using
the current unstable version in combination with pyplusplus to build their 
project
using CastXML instead of GccXML.

I will publish a new pygccxml version (1.7.0) in the next weeks. The package 
name
will not change, and is backwards compatible with gccxml. I will temporarily 
disable
the failing tests when running with CastXML.

Please tell me if I need to notify someone when the new version is out or if 
there
is something I can to to help the packaging. pygccxml will also be available
through pip.

Regards

Michka