C++ help needed for Tide

[Andreas Tille]

Hi,

I have started packaging Tide (a tandard tool for ass-spectroscopy) at

   git://anonscm.debian.org/debian-med/tide.git

Unfortunately these days gcc is more picky about C++ syntax and I was
running into

g++ -ggdb -O6 -DNDEBUG -I./protoobj -g -O2 -fstack-protector-strong -Wformat 
-Werror=format-security -o obj-opt-x86_64/test_spectrum_preprocess.o -c 
src/test_spectrum_preprocess.cc
In file included from src/test_spectrum_preprocess.cc:8:0:
src/records.h: In destructor 'RecordWriter::~RecordWriter()':
src/records.h:85:16: error: 'close' was not declared in this scope
   close(fd_);
^
src/records.h: In destructor 'RecordReader::~RecordReader()':
src/records.h:137:14: error: 'close' was not declared in this scope
 close(fd_);
  ^

Any help would be welcome

Andreas.


PS: Regarding my former related mail about mass-spectroscopy
 
> InsPecT
> ---
>   I found it mentioned on this page
> https://en.wikipedia.org/wiki/List_of_mass_spectrometry_software
>   where it is known that the link is dead.  This page
> http://www.ms-utils.org/wiki/pmwiki.php/Main/SoftwareList
>   lists it as well (the link is really dead)

Preliminary packaging is at

git://anonscm.debian.org/debian-med/inspect.git

I'm seeking a better name for /usr/bin/inspect which is also
in libboost-tools-dev.

-- 
http://fam-tille.de

Re: C++ help needed for Tide

[Sébastien Jodogne]

Hi,

> g++ -ggdb -O6 -DNDEBUG -I./protoobj -g -O2 -fstack-protector-strong -Wformat
> -Werror=format-security -o obj-opt-x86_64/test_spectrum_preprocess.o -c
> src/test_spectrum_preprocess.cc
> In file included from src/test_spectrum_preprocess.cc:8:0:
> src/records.h: In destructor 'RecordWriter::~RecordWriter()':
> src/records.h:85:16: error: 'close' was not declared in this scope
>close(fd_);
> ^
> src/records.h: In destructor 'RecordReader::~RecordReader()':
> src/records.h:137:14: error: 'close' was not declared in this scope
>  close(fd_);
>   ^
> 
> Any help would be welcome

Simply add at the top of "src/records.h":

#include 

You'll also have to add at the top of "src/search.cc" and "src/peptide_mods.cc":

#include 

And finally at the top of "src/modifications.h":

#include 

HTH,
Sébastien-

Packaging pipasic and its dependencies (InsPecT / Tide)

[Andreas Tille]

Hi Martin and Anke,

(I'm writing by wearing my Debian maintainer hut but we can talk about
this also via internal phone - I just want to get Filippo involved since
he might have a good overview abou this topic.)

I have created Debian packaging code for pipasic[1] which creates a
working Debian package - at least if you have installed either InsPecT
or Tide as my experiment with your example data seems to show.

Infortunately your README.txt does not provide a link how to obtain
these programs.  I did some research and hope you can confirm that at
least one of them would be sufficient to use pipasic sensibly.

InsPecT
---
  I found it mentioned on this page
https://en.wikipedia.org/wiki/List_of_mass_spectrometry_software
  where it is known that the link is dead.  This page
http://www.ms-utils.org/wiki/pmwiki.php/Main/SoftwareList
  lists it as well (the link is really dead)

  Do you know any download location - preferably for the source code
  if available at all?  It seems to be a bit suspicious to me that
  you rely on a program that seems to be a bit hidden from sight.


Tide

  I found
http://sourceforge.net/projects/cruxtoolkit/
  and it seems Tide source code could be fetched from SVN directly at
http://sourceforge.net/p/cruxtoolkit/code/HEAD/tree/tide/

  Could you confirm that the code in SVN would work with pipasic?


Kind regards and greetings from Wernigerode

   Andreas.

[1] https://anonscm.debian.org/cgit/debian-med/pipasic.git

-- 
http://fam-tille.de

Re: ITP: sleepyhead -- Software for sleep tracking with focus on CPAP treatment

[Andreas Tille]

Hi Sergio,

On Tue, Sep 29, 2015 at 08:12:23PM -0400, Sergio Durigan Junior wrote:
> 
> A quick look at Blends tells me that maybe this software could fit in
> the 'Medical data' task (because its purpose is to analyse the data
> generated by CPAP machines), although 'Tools' is a good option as well.

I turned this into a "Depends: sleepyhead" in the data task and a
"Suggests: sleepyhead" in tools.  In Blends a package can perfectly show
up in more than one task.  Once the packaging will show up in our VCS it
will be displayed on the according tasks pages under "Packaging has
started and developers might try the packaging code in VCS".
 
> > I would recommend maintaining the package in the Debian Med team and use
> > our VCS (either Git or SVN at your preference).  Here[2] you can find a
> > policy how to join the team and and what workflow we use.
> 
> Sure, no problem.  I will make sure to subscribe to the mailing list and
> request membership of the Debian Med group on Alioth.

Fine.  Just let us know here on this list in case of any trouble.
 
> Thanks for the tips,

You are welcome

   Andreas. 

-- 
http://fam-tille.de

Re: Sponsorship request: snap-aligner

[Michael Crusoe]

On Tue, Sep 29, 2015 at 10:03 PM Charles Plessy  wrote:

> Le Wed, Sep 30, 2015 at 03:42:27AM +, Michael Crusoe a écrit :
> > gbp clone git://anonscm.debian.org/debian-med/snap-aligner.git
>
> Hi Michael,
>
> I found non-Free statements in some files under import/pdclibhdfs/src/,
> for example:
>
> * TITLE: TstReadHdfs.tdprj.xml
>*
> *
>   *
> * Copyright 2009-2010 by Teradata Corporation.
>*
> *
>   *
> * ALL RIGHTS RESERVED.
>*
> *
>   *
> * TERADATA CONFIDENTIAL AND TRADE SECRET
>
> That would make the files unredistributable, but I guess it is just a
> honest
> mistake ?  Can you investigate this further ?
>

Thank you for catching that. They are not used to build, so I've stripped
them out using Files-excluded in debian/copyright.

Alas, I just discovered that tests/bin/ValidateSamFile.jar doesn't contain
its source code and is used by tests/datatest.py & tests/filetest.py so
I've removed that as well and added a patch to not use it.

Should be ready to go now.


> Have a nice day,
>

Thanks!


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

Re: Sponsorship request: snap-aligner

[Andreas Tille]

On Wed, Sep 30, 2015 at 06:02:10AM +, Michael Crusoe wrote:
> 
> Thank you for catching that. They are not used to build, so I've stripped
> them out using Files-excluded in debian/copyright.
> 
> Alas, I just discovered that tests/bin/ValidateSamFile.jar doesn't contain
> its source code and is used by tests/datatest.py & tests/filetest.py so
> I've removed that as well and added a patch to not use it.
> 
> Should be ready to go now.

I'll leave it to Charles except if I do not hear something from him in
the next couple of hours ...

Thanks to both of you

 Andreas.

PS: I have the feeling that we are stress testing ftpmaster with new
packages quite a bit. ;-)

-- 
http://fam-tille.de

Re: Sponsorship request: snap-aligner

[Michael Crusoe]

On Tue, Sep 29, 2015 at 10:11 PM Charles Plessy  wrote:

> Le Wed, Sep 30, 2015 at 04:06:31AM +, Michael Crusoe a écrit :
> > transrate-tools is also ready
> >
> > gbp clone git://anonscm.debian.org/debian-med/transrate-tools.git
>
> Hi Michael,
>
> I think that your "install" file will not work outside the amd64
> architecture:
>
> $ cat transrate-tools.install
> ./obj-x86_64-linux-gnu/src/bam-read /usr/bin/
>
> Maybe you can find a solution similar to what is done in multi-arch
> packages,
> or perhaps a wildcard would be simply enough.
>

A wildcard did the trick, thanks!

The package is ready to go.


>
>
> https://wiki.debian.org/Multiarch/Implementation#Dynamic_debian.2F.2A_files
>
> Cheers,
>
> Charles
>
> --
> Charles Plessy
> Debian Med packaging team,
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan
>

source-is-missing lintian error in orthanc

[Sébastien Jodogne]

Dear all,

While upgrading the orthanc package to the newest upstream version (0.9.4), I 
notice that Lintian reports new "source-is-missing" errors:

==
N: Processing source package orthanc (version 0.9.4+dfsg-1, arch source) ...
E: orthanc source: source-is-missing 
OrthancExplorer/libs/jquery.mobile.simpledialog2.js
E: orthanc source: source-is-missing OrthancExplorer/libs/tree.jquery.js
E: orthanc source: source-is-missing debian/JS/DateJs/src/globalization/el-GR.js
E: orthanc source: source-is-missing debian/JS/DateJs/src/globalization/gu-IN.js
E: orthanc source: source-is-missing debian/JS/DateJs/src/globalization/hi-IN.js
E: orthanc source: source-is-missing debian/JS/DateJs/src/globalization/ka-GE.js
E: orthanc source: source-is-missing debian/JS/DateJs/src/globalization/kn-IN.js
E: orthanc source: source-is-missing 
debian/JS/DateJs/src/globalization/kok-IN.js
E: orthanc source: source-is-missing debian/JS/DateJs/src/globalization/mn-MN.js
E: orthanc source: source-is-missing debian/JS/DateJs/src/globalization/mr-IN.js
E: orthanc source: source-is-missing debian/JS/DateJs/src/globalization/sa-IN.js
E: orthanc source: source-is-missing debian/JS/DateJs/src/globalization/ta-IN.js
E: orthanc source: source-is-missing debian/JS/DateJs/src/globalization/te-IN.js
E: orthanc source: source-is-missing debian/JS/DateJs/src/globalization/th-TH.js
==


Having a look at my personal Lintian reports [1], I then notice that these 
errors are also reported to be present on the version 0.9.3. But, I am sure 
that these errors were not reported back in early August 2015 when the 0.9.3 
package was uploaded.

I have tried to dig into this problem by inspecting the content of the source 
package. Here is the log of the commands I have used to this end:

==
jodogne@unstable:/tmp/lintian$ apt-get source orthanc
Reading package lists... Done
Building dependency tree   
Reading state information... Done
NOTICE: 'orthanc' packaging is maintained in the 'Svn' version control system 
at:
svn://anonscm.debian.org/debian-med/trunk/packages/orthanc/trunk/
Need to get 2,326 kB of source archives.
Get:1 http://ftp.belnet.be/debian/ unstable/main orthanc 0.9.3+dfsg-1 (dsc) 
[2,475 B]
Get:2 http://ftp.belnet.be/debian/ unstable/main orthanc 0.9.3+dfsg-1 (tar) 
[593 kB]
Get:3 http://ftp.belnet.be/debian/ unstable/main orthanc 0.9.3+dfsg-1 (diff) 
[1,731 kB]
Fetched 2,326 kB in 0s (8,241 kB/s)
dpkg-source: info: extracting orthanc in orthanc-0.9.3+dfsg
dpkg-source: info: unpacking orthanc_0.9.3+dfsg.orig.tar.gz
dpkg-source: info: unpacking orthanc_0.9.3+dfsg-1.debian.tar.xz

jodogne@unstable:/tmp/lintian$ cd orthanc-0.9.3+dfsg/

jodogne@unstable:/tmp/lintian/orthanc-0.9.3+dfsg$ ls -l 
OrthancExplorer/libs/jquery.mobile.simpledialog2.js
-rw-r--r-- 1 jodogne jodogne 14278 Aug  7 20:14 
OrthancExplorer/libs/jquery.mobile.simpledialog2.js

jodogne@unstable:/tmp/lintian/orthanc-0.9.3+dfsg$ ls -l 
OrthancExplorer/libs/tree.jquery.js
-rw-r--r-- 1 jodogne jodogne 53290 Aug  7 20:14 
OrthancExplorer/libs/tree.jquery.js

jodogne@unstable:/tmp/lintian/orthanc-0.9.3+dfsg$ ls -l 
debian/JS/DateJs/src/globalization/el-GR.js
-rw-r--r-- 1 jodogne jodogne 6841 Feb 19  2014 
debian/JS/DateJs/src/globalization/el-GR.js
==

So, the files that are reported to be missing are actually present in the 
source package. Could someone provide me guidance about this problem? Is it a 
bug inside Lintian/cruft?

TIA,
Sébastien-


[1] https://lintian.debian.org/maintainer/s.jodo...@gmail.com.html

Processed: retitle 778589 to ITP: berkeley-express -- Streaming quantification for high-throughput sequencing

[Debian Bug Tracking System]

Processing commands for cont...@bugs.debian.org:

> retitle 778589 ITP: berkeley-express -- Streaming quantification for 
> high-throughput sequencing
Bug #778589 {Done: cru...@ucdavis.edu (Michael R. Crusoe)} [wnpp] "ITP: 
berkeley-express -- Streaming quantification for high
Changed Bug title to 'ITP: berkeley-express -- Streaming quantification for 
high-throughput sequencing' from '"ITP: berkeley-express -- Streaming 
quantification for high'
> thanks
Stopping processing here.

Please contact me if you need assistance.
-- 
778589: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=778589
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

Re: source-is-missing lintian error in orthanc

[Sébastien Jodogne]

> > So, the files that are reported to be missing are actually present in the
> > source package.
> 
> ... and this is the problem.  Lintian considers these files not as
> source package since these are minimized (or lintian considers these as
> minimized).  You always need to provide non-minimised, human editable
> form of JS files.  Otherwise the JS is considered as "Binary without
> source".

Thanks for your answer but, actually, these files are human-editable. For 
instance:
https://bitbucket.org/sjodogne/orthanc/src/Orthanc-0.9.3/OrthancExplorer/libs/jquery.mobile.simpledialog2.js
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/orthanc/trunk/debian/JS/DateJs/src/globalization/el-GR.js?view=markup

Regards,
Sébastien-

Re: Maintenance of freeimage over to d-science

[Ghislain Vaillant]

Hi Anton,

I'll be on leave for the next week and can't commit to get this patch 
out soon. Feel free to do it or let the QA team handle it. I will make 
sure to re-sync the packaging repository with theirs when I get back.


Cheers,
Ghislain


On 27/09/15 20:37, Anton Gladky wrote:

Hi Ghislain,

thanks for your work! Please ping me if you need uploading of
this package. Also it would be good to port this security patch
for the Jessie to close that vulnerability.

Best regards

Anton


2015-09-27 16:21 GMT+02:00 Ghislain Vaillant :

Dear all,

Following the discussion in Bug#797165, both Anton and I took the initiative
of moving the maintenance of freeimage over to Debian Science, since quite a
few of our dependencies depend on it.

I have pushed a pristine clone of the collab-maint repository in
git/debian-science/packages/freeimage.git. Now starts the work of updating
the packaging to the latest upstream version (3.17) and review the list of
our patches.

Many thanks to Anton and the Debian QA team for supporting this effort.

Ghislain

Re: source-is-missing lintian error in orthanc

[Andreas Tille]

On Wed, Sep 30, 2015 at 10:40:13AM +0200, Sébastien Jodogne wrote:
> 
> Having a look at my personal Lintian reports [1], I then notice that these 
> errors are also reported to be present on the version 0.9.3. But, I am sure 
> that these errors were not reported back in early August 2015 when the 0.9.3 
> package was uploaded.

May be lintian was not picky enough at this time and was updated to
fetch this?
 
> So, the files that are reported to be missing are actually present in the 
> source package.

... and this is the problem.  Lintian considers these files not as
source package since these are minimized (or lintian considers these as
minimized).  You always need to provide non-minimised, human editable
form of JS files.  Otherwise the JS is considered as "Binary without
source".

Kind regards

  Andreas.

-- 
http://fam-tille.de

Re: source-is-missing lintian error in orthanc

[Andreas Tille]

Hi,

On Wed, Sep 30, 2015 at 11:25:49AM +0200, Sébastien Jodogne wrote:
> > > So, the files that are reported to be missing are actually present in the
> > > source package.
> > 
> > ... and this is the problem.  Lintian considers these files not as
> > source package since these are minimized (or lintian considers these as
> > minimized).  You always need to provide non-minimised, human editable
> > form of JS files.  Otherwise the JS is considered as "Binary without
> > source".
> 
> Thanks for your answer but, actually, these files are human-editable. For 
> instance:
> https://bitbucket.org/sjodogne/orthanc/src/Orthanc-0.9.3/OrthancExplorer/libs/jquery.mobile.simpledialog2.js
> http://anonscm.debian.org/viewvc/debian-med/trunk/packages/orthanc/trunk/debian/JS/DateJs/src/globalization/el-GR.js?view=markup

... then use a lintian-override

Kind regards

  Andreas. 

-- 
http://fam-tille.de

Orthanc 0.9.4

[Sébastien Jodogne]

Hello Andreas,

Thanks to your answers about lintian, I think that Orthanc 0.9.4 is now ready 
for upload [1].

Regards,
Sébastien-


[1] 
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/orthanc/trunk/debian/

Re: Proper package relationships when a project depends on CBLAS

[Felix Salfelder]

On Wed, Sep 30, 2015 at 10:46:51AM +0100, Ghislain Vaillant wrote:
> Then the binary package gets the following dependency:
> Depends: libblas.so.3

just in case: leaving out ${shlibs:Depends} here, you will have to take
care of *all* dependencies manually.

in more complex cases you may wish to set
Depends: ${my_filtered_shlibdeps}
which you may control from d/r. can't remember where i did something
like this :|.

have fun
felix

Re: Proper package relationships when a project depends on CBLAS

[Ghislain Vaillant]

On 29/09/15 18:09, Felix Salfelder wrote:

On Tue, Sep 29, 2015 at 05:49:50PM +0100, Ghislain Vaillant wrote:

what is wrong with a builddep on libopenblas-dev|someotherblas-dev?

do you want to discard the second option in case the first is available
(don't know how to do that)?


If I use say libopenblas-dev | libatlas-dev, then the generated
binary package will have a Depends field with either
libopenblas.so.X or libatlas.so.X.


i assume this dependency is generated by dh_shlibdeps and your control
file lists ${shlibs:Depends} in the list of binary package dependencies.
for sure you can exchange that for whatever you please, e.g.
libopenblas.so.X | libatlas.so.X


Instead, I should probably have
libblas.so.X which can be updated via update-alternatives to any of
these implementations.


if there is a virtual package that depends on one of the above, then
sure, depend on that one.


Now I understand. I have replaced this dependency with:
BuildDepends: libblas-dev | libblas.so

Whereby libblas.so can be provided by libopenblas-dev or libatlas-dev.

Then the binary package gets the following dependency:
Depends: libblas.so.3

Which may be provided by libopenblas, libatlas or libblas, via 
update-alternatives.



Or should I actually care?


this is up to you. (but yes, sounds fun).


One learns something everyday :-)

Many thanks Felix for your pointers.

Ghis

Re: update: automatic backports

[Andreas Tille]

On Wed, Sep 30, 2015 at 02:19:54AM -0700, Afif Elghraoui wrote:
> ...
> So it looks like I can link something from these approaches to the
> testing migration tracking. Right now, the tracking is implemented as
> watching and parsing the emails.

Thanks for the update.  Just let us know if there is something to
test.

Kind regards

  Andreas.

-- 
http://fam-tille.de

Re: Maintenance of freeimage over to d-science

[Anton Gladky]

OK, so should I commit to QA repo or debian-science.

Anton

Am Mittwoch, 30. September 2015 schrieb Ghislain Vaillant :

> Hi Anton,
>
> I'll be on leave for the next week and can't commit to get this patch out
> soon. Feel free to do it or let the QA team handle it. I will make sure to
> re-sync the packaging repository with theirs when I get back.
>
> Cheers,
> Ghislain
>
>
> On 27/09/15 20:37, Anton Gladky wrote:
>
>> Hi Ghislain,
>>
>> thanks for your work! Please ping me if you need uploading of
>> this package. Also it would be good to port this security patch
>> for the Jessie to close that vulnerability.
>>
>> Best regards
>>
>> Anton
>>
>>
>> 2015-09-27 16:21 GMT+02:00 Ghislain Vaillant :
>>
>>> Dear all,
>>>
>>> Following the discussion in Bug#797165, both Anton and I took the
>>> initiative
>>> of moving the maintenance of freeimage over to Debian Science, since
>>> quite a
>>> few of our dependencies depend on it.
>>>
>>> I have pushed a pristine clone of the collab-maint repository in
>>> git/debian-science/packages/freeimage.git. Now starts the work of
>>> updating
>>> the packaging to the latest upstream version (3.17) and review the list
>>> of
>>> our patches.
>>>
>>> Many thanks to Anton and the Debian QA team for supporting this effort.
>>>
>>> Ghislain
>>>
>>

-- 

Anton

update: automatic backports

[Afif Elghraoui]

Hi, all,
Continuing from the previous discussions [1-2], I have just a little bit
to report (though I have not worked on it very much since then,
unfortunately)

My repository is now published at
http://anonscm.debian.org/cgit/users/afif-guest/backportd.git/

I appreciate the neurodebian people giving some comments about their
workflow. I looked at the Debian Med meeting minutes from Debconf [3]
and have also discovered Ubuntu's backportpackage script [4] (in the
ubuntu-dev-tools package).

So it looks like I can link something from these approaches to the
testing migration tracking. Right now, the tracking is implemented as
watching and parsing the emails.

regards
Afif

1. https://lists.debian.org/debian-med/2015/08/msg00063.html
2. https://lists.debian.org/debian-med/2015/08/msg00154.html
3. https://people.debian.org/~tille/talks/20150821_debconf_med/index_en.html
4. http://manpages.ubuntu.com/manpages/trusty/man1/backportpackage.1.html

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

Bug#800335: cereal: source package name conflicts

[Michael Crusoe]

Oops, I thought I had renamed the source package to libcereal.

What's the best way to correct this situation? The package is already in
the NEW queue: http://ftp-master.debian.org/new/cereal_1.1.2-1.html