Re: Chances for cooperation between OSDDLinux and Debian

[Steffen Möller]

Dear Dr Raghava,

The situation you are describing sounds very familiar. And all
you write supports this idea of

 - using the Debian/Ubuntu/Bio-Linux packages for Bioinformatics
   that are already provided, i.e. do not package anything
   redundant

 - focus resources by self-adding the .deb files of particular
   demand that are not yet redistributed by the distribution

The packages gathered via Debian Med may be interpreted as a basis
of your distribution that your distro extends for the best-possible
benefit of your users. Consequently, even when you do not find the time
yourself to perform an update of your packages, chances are high that
the orchestrated-by-Debian-Med regular Bioinformatics package of your
distribution have been updated. Forwarding those will be of immediate
value to your users without respective efforts for maintenance on your side.

Another positive aspect of the Debian Med effort is that your
"more-biologist" group members find someone to partner up for the
creation of a package. And it is fun, too. Software redistributed
by Debian Med is shown here http://blends.debian.org/med/tasks/index

With kind regards,

Steffen Möller


On 18.10.2015 11:26, G. P. S. Raghava wrote:
> Dear Andreasa
> Thanks for email, You are right we have not added anything in last two years. 
> It is all due to time constrained, my team is mainly dominated by biologist 
> rather than computer professional. My team is busy in developing web-based 
> services (average 15 servers per year) which is part of there research 
> publications. Last time two year back, we spend nearly three months to 
> develop OSDDlinux. I am trying to get help from companies but not getting 
> help in packaging. Hope in few months we will have some progress as we are 
> planing to focus again on OSDDlinux  (adding more software and packaging 
> software).
>  
> 
> With best wishes & regards
> 
> Raghava
> == 
> # Dr G P S Raghava (FASc, FNASc), Head Bioinformatics Centre   # 
> # Institute of Microbial Technology, Sector-39A, Chandigarh, India   # 
> # Phone: +91-172-2690557, Fax: +91-172-2690632 # 
> # Eadd: http://www.imtech.res.in/raghava/   ragh...@imtech.res.in # 
> #= 
> Wiki:  http://en.wikipedia.org/wiki/Gajendra_Pal_Singh_Raghava
> GS:  http://scholar.google.co.in/citations?hl=en=XK5GUiYJ
> 
> 
> 
> On 18-Oct-2015, at 11:55, Andreas Tille  wrote:
> 
> Hi again,
> 
> I would really like to refresh this mail exchange from years ago.  I
> keep on thinking that OSDDLinux and Debian could work together as
> similarly successfully as BioLinux and Debian.  I noticed that the
> packages in your package pool[1] were not updated nearly two years.  Is
> this a sign of some kind of stable release and you have a development
> area somewhere?  Do you have some repository of source packages where we
> could work with and start some integration into Debian?  Please consider
> cooperation with Debian to join manpower.
> 
> Kind regards
> 
>Andreas.
> 
> [1] http://osddlinux.osdd.net/repo/ngs/
> 
> On Sun, Feb 02, 2014 at 06:03:00PM +0100, Andreas Tille wrote:
>> Hi again,
>>
>> we had a quite successful sprint and I teached packaging to five people
>> which are now busy packaging their own stuff.  This all goes into
>> official Debian and finally also Ubuntu + BioLinux will profit from
>> this.  I'm not sure whether I was clear in my first contact to you and
>> the OSDDlinux team so I try to rephrase my plan:  We could integrate all
>> programs you are using in OSDDlinux (provided they have a free license)
>> straight into Debian which might save you a lot of extra work.  The way
>> to do this is to inject your packaging in our common platform
>> alioth.debian.org and than Debian Developers from Debian Med team can
>> sponsor this to official Debian mirror after checking its policy
>> conformity.  This workflow is quite established with BioLinux and you
>> youst need to confirm that you like this plan and we will work out
>> the technical details how to go from here.
>>
>> Kind regards
>>
>> Andreas.
>>
>> On Thu, Jan 30, 2014 at 08:17:09PM +0100, Andreas Tille wrote:
>>> Hi Raghava,
>>>
>>> considering that the Debian Med sprint will start tomorrow (I'm just on
>>> my way to Aberdeen) nobody from your team will join.  I'd suggest we
>>> could meet in IRC to find some way to work together efficiently to make
>>> sure Debian Med can support your work as best as possible.
>>>
>>> Kind regards
>>>
>>>  Andreas.
>>>
>>> On Tue, Oct 15, 2013 at 10:20:08PM +0530, G P S Raghava wrote:
 Dear Andreas
 Thanks for your email and offer for cooperation. We are very much 
 interested to work with debian-med and biolinux, as all three debian-med , 
 biolinux and OSDDlinux have common object to provide service to the 
 scientific community. I will write detail email to 

Re: Chances for cooperation between OSDDLinux and Debian

[Andreas Tille]

Hi again,

I would really like to refresh this mail exchange from years ago.  I
keep on thinking that OSDDLinux and Debian could work together as
similarly successfully as BioLinux and Debian.  I noticed that the
packages in your package pool[1] were not updated nearly two years.  Is
this a sign of some kind of stable release and you have a development
area somewhere?  Do you have some repository of source packages where we
could work with and start some integration into Debian?  Please consider
cooperation with Debian to join manpower.

Kind regards

Andreas.

[1] http://osddlinux.osdd.net/repo/ngs/

On Sun, Feb 02, 2014 at 06:03:00PM +0100, Andreas Tille wrote:
> Hi again,
> 
> we had a quite successful sprint and I teached packaging to five people
> which are now busy packaging their own stuff.  This all goes into
> official Debian and finally also Ubuntu + BioLinux will profit from
> this.  I'm not sure whether I was clear in my first contact to you and
> the OSDDlinux team so I try to rephrase my plan:  We could integrate all
> programs you are using in OSDDlinux (provided they have a free license)
> straight into Debian which might save you a lot of extra work.  The way
> to do this is to inject your packaging in our common platform
> alioth.debian.org and than Debian Developers from Debian Med team can
> sponsor this to official Debian mirror after checking its policy
> conformity.  This workflow is quite established with BioLinux and you
> youst need to confirm that you like this plan and we will work out
> the technical details how to go from here.
> 
> Kind regards
> 
>  Andreas.
> 
> On Thu, Jan 30, 2014 at 08:17:09PM +0100, Andreas Tille wrote:
> > Hi Raghava,
> > 
> > considering that the Debian Med sprint will start tomorrow (I'm just on
> > my way to Aberdeen) nobody from your team will join.  I'd suggest we
> > could meet in IRC to find some way to work together efficiently to make
> > sure Debian Med can support your work as best as possible.
> > 
> > Kind regards
> > 
> >   Andreas.
> > 
> > On Tue, Oct 15, 2013 at 10:20:08PM +0530, G P S Raghava wrote:
> > > Dear Andreas
> > > Thanks for your email and offer for cooperation. We are very much 
> > > interested to work with debian-med and biolinux, as all three debian-med 
> > > , biolinux and OSDDlinux have common object to provide service to the 
> > > scientific community. I will write detail email to you soon.
> > >  
> > > With best wishes & regards
> > > 
> > > Raghava
> > > #=#
> > > # Dr G P S Raghava FASc, FNASc, Scientist & Head Bioinformatics Centre  #
> > > # CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh, India  
> > >#
> > > # Phone: +91-172-2690557, 0172-6665450 ; Fax: +91-172-2690632   #
> > > # Eadd: http://www.imtech.res.in/raghava/   Email: ragh...@imtech.res.in  
> > >  #
> > > #=# 
> > > 
> > > Google Scholar: 
> > > http://scholar.google.co.in/citations?user=XK5GUiYJ=en
> > > 
> > > On 15-Oct-2013, at 2:36 PM, Andreas Tille wrote:
> > > 
> > > > Hi,
> > > > 
> > > > I'm contacting you on behalf of the Debian Med team which has the goal
> > > > to package any Free Software that is relevant for medical care straight
> > > > into Debian.[1]
> > > > 
> > > > Your OSDDlinux looks like an exciting implementation of our idea to
> > > > bring Debian to the end user.  Our goal is to prepare as much as
> > > > possible straight into Debian to make your work as easy as possible - in
> > > > an optimal situation you should be able to autogenerate your
> > > > distribution straight from the Debian package pool so your content is
> > > > actually Debian and you just need to care for some user oriented
> > > > customisation, support and contact to your users.  I hope you might like
> > > > this idea - at least the BioLinux distriution[2] which in principle has
> > > > the very same goal like you just for a different target user group is
> > > > happy about the cooperation we established since more than three years.
> > > > 
> > > > If you look at our so called web sentinel for instance on the biology
> > > > section[3] you will find a lot of matches to your NGS page[4] (and on
> > > > other pages - just to mention an example).  Our goal would be to work
> > > > on the missings between your page and our software pool to enable you
> > > > to profit directly from the work done inside Debian.
> > > > 
> > > > The cooperation with BioLinux developers was established in a way that
> > > > we are working inside the very same version control system(s - we are
> > > > using Git or SVN at the developers preference).  So changes made in
> > > > BioLinux will immediately forewardet into the Debian package and if a
> > > > Debian developer changes something this directly leads to an enhancement
> > > > inside BioLinux.  We regard this as a win-win-situation to save time and
> > > > man 

Re: Packaging fsa for Debian

[Andreas Tille]

Ping,

is there any active development of fsa and could anybody please answer
the questions below?

Kind regards

Andreas.

On Mon, Aug 18, 2014 at 03:11:24PM +0200, Andreas Tille wrote:
> Hi,
> 
> I'm writing you on behalf of the Debian Med team which is interested in
> packaging fsa for Debian since it fits nicely into all other software we
> assembled for biological research inside main Debian[1].  Specifically
> the fact that it is recommended when using t-coffee has inspired me to
> do the packaging work.
> 
> The Debian build process is designet to run a test suite if available
> and so it also tried to run the tests target of fsa.  However, it seems
> you do not provided the files needed to run the test suite in your
> download tarball.  I just got:
> 
>No rule to make target 'apps/isect_d.unmappable.bash', needed by 
> 'apps/isect_d.unmappable.bash.log'.  Stop.
> 
> Is there any chance to include the full or at least a stripped down test
> suite into the tarball?
> 
> Moreover I tried to create manpages for all binaries which were created
> by the build process via help2man.  However I failed for the following
> executables
> 
>   isect_mercator_alignment_gff
>   map_coords
>   map_gff_coords
>   slice_mercator_alignment
> 
> Simply calling these scripts either plain or with --help option endet up
> in
> 
>   Segmentation fault
> 
> I think this should be fixed.
> 
> Kind regards and thanks for providing fsa as free software
> 
>Andreas.
> 
> [1] http://blends.debian.org/med/tasks/bio#fsa
> 
> -- 
> http://fam-tille.de
> 
> 
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> To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
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> 
> 

-- 
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Re: Any volunteer to take some simple R packages as packaging training?

[Andreas Tille]

Hi,

I'm going through old mails in my mailbox and I'm wondering whether
somebody wants to work on these very simple targets.  There was some
response from Johannes Schaffrath a year ago but no further action.

These could be nice projects for Mentoring of the Month and I think
the packages are simple enough to take way less than one month.

Kind regards

  Andreas.

On Thu, Sep 11, 2014 at 01:49:49PM +0200, Andreas Tille wrote:
> Hi,
> 
> according to
> 
>
> http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-ebimage/trunk/debian/changelog?revision=17994=markup
> 
> we need to package
> 
>   r-cran-tiff: http://cran.r-project.org/web/packages/tiff/index.html
>   r-cran-jpeg: http://cran.r-project.org/web/packages/jpeg/index.html
>   r-cran-png: http://cran.r-project.org/web/packages/png/index.html
> 
> to get r-bioc-ebimage packaged.  Usually R packages are quite simple and
> thus a good learning example.  I do not want to spoil the fun of some
> newcomer and do it myself - so any takers for these?  Any help in case
> of trouble is granted for sure.
> 
> Kind regards
> 
>Andreas.
> 
> -- 
> http://fam-tille.de
> 
> 
> -- 
> 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/2014094949.gt19...@an3as.eu
> 
> 

-- 
http://fam-tille.de

Re: packaging UCSC kent tools for debian-med

[Andreas Tille]

Hi,

are there any news about versioned tarballs of your software at
genome-source.cse.ucsc.edu ?

Kind regards

   Andreas.

On Wed, Aug 27, 2014 at 11:04:13AM +0200, Andreas Tille wrote:
> Hi again,
> 
> please see my additions inline!
> 
> 
> On Wed, Aug 27, 2014 at 10:52:35AM +0200, Andreas Tille wrote:
> > Hi Hiram,
> > 
> > I hope you don't mind if I'm putting Debian Med list in the discussion
> > which I would like you to do in pure technical discussion as well.
> > 
> > On Wed, Aug 27, 2014 at 12:00:59AM -0700, Hiram Clawson wrote:
> > > Good Evening Andreas:
> > > 
> > > I'm curious if there would be a way to fit this building procedure
> > > into the Debian-Med project:
> > > 
> > >
> > > http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README
> > > 
> > > Note steps 1, 2, 3 near the top of the README after the 'System 
> > > Requirements'
> > > discussion.
> > > 
> > > I fully realize this isn't they way packages are supposed to work, but at
> > > this time, this is the best we have.
> > 
> > Simply from reading the README I can not see anything unusual.  Step 1
> > (fetching the tarball) is totally normal workflow,
> 
> Some correction to what I said here:  Please provide a *versioned*
> tarball!  Every tarball should have a version to be able to detect updates.
> 
> Moreover once I have checked the tarball I realised that the problematic
> license which was discussed previously[0] remains.  So *if* this software
> should be distributed by Debian this needs to be fixed first.
> 
> > step 2 is cd-ing to
> > the unpackaged dir and call make is also pretty normal except that this
> > make call is done by the debhelper tools.  The only difference is step 3
> > where we do not move files to /usr/local but rather into /usr/bin inside
> > the Debian package.
> > 
> > > Perhaps there could be a way to
> > > encapsulate these first three steps into some kind of building/packaging
> > > business that would satisfy the standard build and packaging procedures ?
> > 
> > Yes, for sure.  That's the day job of a Debian packager.  Do you want to
> > learn how to do this?  If yes we could offer mentoring in the so called
> > Mentoring of the Month[1] effort.  While there is right now the
> > September slot occupied I would try hard to help you as well since if we
> > want to get these tools included (and I would really love to see this)
> > we need to start right now.
> > 
> > So are you able to invest some time slots into the packaging and want to
> > work together with us please subscribe this mailing lists (links should be
> > given on the Wiki page[1]) and ask for help here in case of trouble or
> > if you need some kickstart help.
> > 
> > Thanks for your interest in Debian Med
> > 
> >   Andreas.
> > 
> > [1] https://wiki.debian.org/DebianMed/MoM
> 
> [0] 
> http://lists.alioth.debian.org/pipermail/debian-med-packaging/2014-March/025520.html
> 
> -- 
> http://fam-tille.de
> 
> 
> -- 
> To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
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> 
> 

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Re: Packaging source code for Debian Distributions

[Andreas Tille]

Hi again,

since my last mail is 1.5 years ago and one stable Debian release
inbetween.  I wonder whether you might consider to adaptthe license of
blat and the tools around for distribution in Debian.

Kind regards

Andreas.

On Fri, Feb 28, 2014 at 09:46:55AM +0100, Andreas Tille wrote:
> Hi,
> 
> since Jim has given permission to quote him on the list I'll answer here.
> 
> On Thu, Feb 27, 2014 at 12:47:42AM -0800, Jim Kent wrote:
> > Hi Hiram and Ann - I'd like to introduce you to Andreas Tille.  Andreas has
> > been working with me to get blat set up for easy compile and install under
> > Debian.  He is part of a project to get biomedical software, including
> > software with some monetary licensing requirements, more accessible.
> 
> To learn what packages in the field of biology we are maintaining inside
> official Debian you might like to have a look at our tasks list:
> 
>http://blends.debian.org/med/tasks/bio
>http://blends.debian.org/med/tasks/bio-dev
> 
> Please note that packages with licensing restrictions according the
> Debian Free Software Guidelines[1] are not part of the Debian
> distribution and also are not included in the metapackages (med-bio and
> med-bio-dev which can be used to install all the software inside Debian
> in one rush).  As long as the license does not permit distribution at
> all it could be packaged and uploaded to non-free and users might be
> able to download from there.
> 
> > He has some interest in doing something similar for the entire UCSC source
> > tree.   Since making our command line software more accessible is one of
> > the aims of our current NHGRI grant,  I think the timing is near perfect
> > for us to work with him on this.
> 
> It would be really cool to work together with you.  We have quite good
> experience by working together with upstream developers.  there is also
> the effort "Mentoring of the Month"
> 
>   https://wiki.debian.org/DebianMed/MoM
> 
> which might help you.
> 
> > Hiram,  could you correspond with Andreas and talk tech and build process
> > with him, and generally get to know him?
> 
> I would really prefer to communicate via the mailing list exclusively
> since we are a team and on one hand we get more input from other team
> members and on the other hand it might be interesting for other people
> learning about your packaging effort soon.
> 
> > One thing we'd need to do that Andreas couldn't,  would be to reorganize
> > the directory structure a bit to make understanding what part is available
> > under what license less of a labyrinth.  They would need to stick the
> > freeware, the UCSC gets $$ for commercial licenses, and the Kent
> > Informatics gets $$ for commercial licenses bits into separate packages,
> >  and I've long felt like we should attempt at least to organize the
> > directory structure to make this more clear.   Something along the line of
> >   kent/src/hg   ->   src/ucsc
> >   kent/src/jkOwnLib -> src/kentInformatics
> >   kent/src/lib   ->src/freeware
> > Where src/inc and src/utils would end up in freeware as well, as well as
> > hg/autoSql and a few other things that are currently out of place.  The
> > ameme, blat, and waba would end up in kentInformatics as well.
> 
> I perfectly agree that this reorganisation would be a very helpful thing
> to do before we start packaging.  I would also recommend to rework the
> build system (either automake or cmake) to enable
> 
>a) dynamic & static libraries (since in Debian we usually separate
>   these in different binary packages)
>b) portability to different architectures (since in Debian the packages
>   are autobuilded for different architectures and this is most easily
>   done if the build system is able to deal with different architectures
>   themselves)
> 
> > Anyway,  Andreas doesn't need to hear all the details of what goes where,
> >  though if has ideas for better high level directory names, it'd be good to
> > hear.
> 
> Finally we need some sensibly craftet versioned release tarballs.  It
> might make sense to create some library releases first and the releasing
> application releases which are using these libraries.
> 
> > Ann, if you could budget some of Hiram's time to work on this it'd be very
> > helpful.   I don't think this is the must be done right away sort of thing,
> >  but once hg38, the new reference genome build,  settles down a bit,  maybe
> > in a 3-6 month time frame,  it would be something Hiram might have time and
> > inclination to spend some serious time on.  If we can keep Andreas'
> > interest we might get some free help with the work too!
> > 
> > Take care,
> >  Jim
> 
> Thanks for your cooperation
> 
>  Andreas.
> 
> [1] https://www.debian.org/social_contract#guidelines
> 
> -- 
> http://fam-tille.de
> 
> 
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> with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
> 

Re: Chances for cooperation between OSDDLinux and Debian

[G. P. S. Raghava]

Dear Andreasa
Thanks for email, You are right we have not added anything in last two years. 
It is all due to time constrained, my team is mainly dominated by biologist 
rather than computer professional. My team is busy in developing web-based 
services (average 15 servers per year) which is part of there research 
publications. Last time two year back, we spend nearly three months to develop 
OSDDlinux. I am trying to get help from companies but not getting help in 
packaging. Hope in few months we will have some progress as we are planing to 
focus again on OSDDlinux  (adding more software and packaging software).
 

With best wishes & regards

Raghava
== 
# Dr G P S Raghava (FASc, FNASc), Head Bioinformatics Centre   # 
# Institute of Microbial Technology, Sector-39A, Chandigarh, India   # 
# Phone: +91-172-2690557, Fax: +91-172-2690632 # 
# Eadd: http://www.imtech.res.in/raghava/   ragh...@imtech.res.in # 
#= 
Wiki:  http://en.wikipedia.org/wiki/Gajendra_Pal_Singh_Raghava
GS:  http://scholar.google.co.in/citations?hl=en=XK5GUiYJ



On 18-Oct-2015, at 11:55, Andreas Tille  wrote:

Hi again,

I would really like to refresh this mail exchange from years ago.  I
keep on thinking that OSDDLinux and Debian could work together as
similarly successfully as BioLinux and Debian.  I noticed that the
packages in your package pool[1] were not updated nearly two years.  Is
this a sign of some kind of stable release and you have a development
area somewhere?  Do you have some repository of source packages where we
could work with and start some integration into Debian?  Please consider
cooperation with Debian to join manpower.

Kind regards

   Andreas.

[1] http://osddlinux.osdd.net/repo/ngs/

On Sun, Feb 02, 2014 at 06:03:00PM +0100, Andreas Tille wrote:
> Hi again,
> 
> we had a quite successful sprint and I teached packaging to five people
> which are now busy packaging their own stuff.  This all goes into
> official Debian and finally also Ubuntu + BioLinux will profit from
> this.  I'm not sure whether I was clear in my first contact to you and
> the OSDDlinux team so I try to rephrase my plan:  We could integrate all
> programs you are using in OSDDlinux (provided they have a free license)
> straight into Debian which might save you a lot of extra work.  The way
> to do this is to inject your packaging in our common platform
> alioth.debian.org and than Debian Developers from Debian Med team can
> sponsor this to official Debian mirror after checking its policy
> conformity.  This workflow is quite established with BioLinux and you
> youst need to confirm that you like this plan and we will work out
> the technical details how to go from here.
> 
> Kind regards
> 
> Andreas.
> 
> On Thu, Jan 30, 2014 at 08:17:09PM +0100, Andreas Tille wrote:
>> Hi Raghava,
>> 
>> considering that the Debian Med sprint will start tomorrow (I'm just on
>> my way to Aberdeen) nobody from your team will join.  I'd suggest we
>> could meet in IRC to find some way to work together efficiently to make
>> sure Debian Med can support your work as best as possible.
>> 
>> Kind regards
>> 
>>  Andreas.
>> 
>> On Tue, Oct 15, 2013 at 10:20:08PM +0530, G P S Raghava wrote:
>>> Dear Andreas
>>> Thanks for your email and offer for cooperation. We are very much 
>>> interested to work with debian-med and biolinux, as all three debian-med , 
>>> biolinux and OSDDlinux have common object to provide service to the 
>>> scientific community. I will write detail email to you soon.
>>> 
>>> With best wishes & regards
>>> 
>>> Raghava
>>> #=#
>>> # Dr G P S Raghava FASc, FNASc, Scientist & Head Bioinformatics Centre  #
>>> # CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh, India
>>>  #
>>> # Phone: +91-172-2690557, 0172-6665450 ; Fax: +91-172-2690632   #
>>> # Eadd: http://www.imtech.res.in/raghava/   Email: ragh...@imtech.res.in   #
>>> #=# 
>>> 
>>> Google Scholar: 
>>> http://scholar.google.co.in/citations?user=XK5GUiYJ=en
>>> 
>>> On 15-Oct-2013, at 2:36 PM, Andreas Tille wrote:
>>> 
 Hi,
 
 I'm contacting you on behalf of the Debian Med team which has the goal
 to package any Free Software that is relevant for medical care straight
 into Debian.[1]
 
 Your OSDDlinux looks like an exciting implementation of our idea to
 bring Debian to the end user.  Our goal is to prepare as much as
 possible straight into Debian to make your work as easy as possible - in
 an optimal situation you should be able to autogenerate your
 distribution straight from the Debian package pool so your content is
 actually Debian and you just need to care for some user oriented
 customisation, support and contact to 

Re: [po...@debian.org: Bug#802172: ismrmrd: FTBFS on several arches]

[Ghislain Vaillant]

I will, sorry for forgetting to push.

I will forward the bug upstream to get the test suite fixed, assuming 
upstream cares for these architectures.


Ghis


On 18/10/15 07:38, Andreas Tille wrote:

Hi Ghislain,

I guess you will care about this bug.  I noticed that the repository in
Debian Med is not containing 1.3.1-1.  Could you please push the latest
state?

Thanks

  Andreas.

- Forwarded message from Emilio Pozuelo Monfort  -

Date: Sun, 18 Oct 2015 02:45:53 +0200
From: Emilio Pozuelo Monfort 
To: sub...@bugs.debian.org
Subject: Bug#802172: ismrmrd: FTBFS on several arches
X-Debian-PR-Message: report 802172
X-Debian-PR-Package: src:ismrmrd
X-Debian-PR-Keywords:
X-Debian-PR-Source: ismrmrd

Source: ismrmrd
Version: 1.3.1-1
Severity: serious

Your package failed to build on several architectures. Here's an excerpt from
the armel build:

*** 546 failures detected in test suite "ISMRMRD Unit Tests"
make[4]: *** [tests/CMakeFiles/check] Error 201

All logs available at:

https://buildd.debian.org/status/logs.php?pkg=ismrmrd=1.3.1-1

Emilio

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- End forwarded message -

Re: packaging UCSC kent tools for debian-med

[Hiram Clawson]

Good Morning Andreas:

Yes, the versioned tar balls can be seen here:

http://hgdownload.cse.ucsc.edu/admin/exe/

Note the userApps.vNNN.src.tgz files
with the newest one always as simply userApps.src.tgz

These binaries can be built thusly:

rm -fr userApps
wget --timestamping  http://hgdownload.cse.ucsc.edu/admin/exe/userApps.src.tgz
tar xvzf userApps.src.tgz
cd userApps
MAKE="make -j 24" make -j 24 > make.log 2>&1

Resulting binaries end up in userApps/bin/

The versioned tarballs do not unpack into unique named directories,
they unpack in the same 'userApps' binary:

This is the same result:

rm -fr userApps
wget --timestamping  
http://hgdownload.cse.ucsc.edu/admin/exe/userApps.v323.src.tgz
tar xvzf userApps.v323.src.tgz
cd userApps
MAKE="make -j 24" make -j 24 > make.log 2>&1

Please note the userApps/README file for expected system requirements
and alternative build procedures using 'git', for example:

 
http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/userApps/README

This code will not compile nor function on sparc or alpha machines.
Only x86_64 and Mac OSX have been tested.  There is no comprehensive test suite,
although some binaries do have a 'make test' target but it is all a manual
procedure, nothing automatic.

--Hiram

On 10/18/15 12:12 AM, Andreas Tille wrote:

Hi,

are there any news about versioned tarballs of your software at
genome-source.cse.ucsc.edu ?

Kind regards

Andreas.

On Wed, Aug 27, 2014 at 11:04:13AM +0200, Andreas Tille wrote:

Hi again,

please see my additions inline!


On Wed, Aug 27, 2014 at 10:52:35AM +0200, Andreas Tille wrote:

Hi Hiram,

I hope you don't mind if I'm putting Debian Med list in the discussion
which I would like you to do in pure technical discussion as well.

On Wed, Aug 27, 2014 at 12:00:59AM -0700, Hiram Clawson wrote:

Good Evening Andreas:

I'm curious if there would be a way to fit this building procedure
into the Debian-Med project:


http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README

Note steps 1, 2, 3 near the top of the README after the 'System Requirements'
discussion.

I fully realize this isn't they way packages are supposed to work, but at
this time, this is the best we have.


Simply from reading the README I can not see anything unusual.  Step 1
(fetching the tarball) is totally normal workflow,


Some correction to what I said here:  Please provide a *versioned*
tarball!  Every tarball should have a version to be able to detect updates.

Moreover once I have checked the tarball I realised that the problematic
license which was discussed previously[0] remains.  So *if* this software
should be distributed by Debian this needs to be fixed first.


step 2 is cd-ing to
the unpackaged dir and call make is also pretty normal except that this
make call is done by the debhelper tools.  The only difference is step 3
where we do not move files to /usr/local but rather into /usr/bin inside
the Debian package.


Perhaps there could be a way to
encapsulate these first three steps into some kind of building/packaging
business that would satisfy the standard build and packaging procedures ?


Yes, for sure.  That's the day job of a Debian packager.  Do you want to
learn how to do this?  If yes we could offer mentoring in the so called
Mentoring of the Month[1] effort.  While there is right now the
September slot occupied I would try hard to help you as well since if we
want to get these tools included (and I would really love to see this)
we need to start right now.

So are you able to invest some time slots into the packaging and want to
work together with us please subscribe this mailing lists (links should be
given on the Wiki page[1]) and ask for help here in case of trouble or
if you need some kickstart help.

Thanks for your interest in Debian Med

   Andreas.

[1] https://wiki.debian.org/DebianMed/MoM


[0] 
http://lists.alioth.debian.org/pipermail/debian-med-packaging/2014-March/025520.html

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Bug#800337: marked as done (ITP: libspdlog-dev -- Very fast, header only, C++ logging library)

[Debian Bug Tracking System]

Your message dated Sun, 18 Oct 2015 13:00:24 +
with message-id 
and subject line Bug#800337: fixed in spdlog 1.4-1
has caused the Debian Bug report #800337,
regarding ITP: libspdlog-dev -- Very fast, header only, C++ logging library
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
800337: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=800337
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Owner: "Debian Med Team" 
Severity: wishlist
X-Debbugs-CC:  debian-med@lists.debian.org

* Package name: libspdlog-dev
  Version : 1.4
  Upstream Author : Gabi Melman 
* URL : https://github.com/COMBINE-lab/spdlog
* License : MIT
  Programming Lang: C++
  Description : Very fast, header only, C++ logging library

Features: Very fast - performance is the primary goal; Headers only; No
dependencies - just copy and use; call style using the excellent cppformat
library; ostream call style is supported too; Optional extremely fast
asynchronous mode - using lockfree queues and other tricks to reach
millions  of calls/sec; Custom formatting; Multi/Single threaded loggers;
Easily extendable with custom log targets (just implement a single function
in the sink interface). Severity based filtering - threshold levels can be
modified in runtime as well as in compile time.

Various log targets:
Rotating log files, Daily log files, Console logging, Linux syslog.

This package is a dependency for salmon.

This package will be maintained as part of the Debian Med packaging team.
--- End Message ---
--- Begin Message ---
Source: spdlog
Source-Version: 1.4-1

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

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

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 800...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Michael R. Crusoe  (supplier of updated spdlog package)

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


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 18 Sep 2015 20:31:46 -0700
Source: spdlog
Binary: libspdlog-dev
Architecture: source amd64
Version: 1.4-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Description:
 libspdlog-dev - Very fast, header only, C++ logging library
Closes: 800337
Changes:
 spdlog (1.4-1) unstable; urgency=low
 .
   * Initial release (Closes: #800337)
Checksums-Sha1:
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libspdlog-dev_1.4-1_amd64.deb
Files:
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 dc99d8085cda5f872fd77ba09b4a496f 2644 libdevel optional 
spdlog_1.4-1.debian.tar.xz
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libspdlog-dev_1.4-1_amd64.deb

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Sponsoring request GDCM 2.6

[Gert Wollny]

On Sat, 2015-10-17 at 23:56 +0200, Andreas Tille wrote:
> I'd recommend
> 
>Files-Excluded: *.lib

That was exactly what I was hoping to find :) 

All the changes are now in the subversion tree 

  svn://svn.debian.org/debian-med/trunk/packages/gdcm/trunk


The ChangeLog is quite extensive, most notable: 

 * new upstream  
 * transition to VTK6 
 * java bindings disabled for now (depend on vtk6)
 * redo parts of d/copyright 

and I added my name to the uploaders for possible future work. 

It is possible that this upload also fixes #767217 (arm64 build) and 
#746268 (hundreds of "sh: 1: dot: not found" messages), however the
first I can not test and for the second I didn't stare long enough at
the pbuilder output. 

There are info-tags for two spelling errors and three hardening-no
-fortify-functions that I didn't override. 

Best, 
Gert