Re: Primer3

2016-06-26 Thread Canberk Koç 
Hello Andreas,

I manage to finish fixes can you control them please . If i do something
wrong i work on it immediately.

Thanks for guidence and help.

Best Regards



Canberk Koç
[image: https://]about.me/canberkkoc


2016-06-26 21:33 GMT+03:00 Canberk Koç :

> Hello Andreas,
>
> I must go to hospital due to  an emergency situation. Now i'll look for
> clean up these files.
>
> Best Regards
>
> Canberk Koç
> www.about.me/canberkkoc
> 26 Haz 2016 15:12 tarihinde "Andreas Tille"  yazdı:
>
> On Sun, Jun 26, 2016 at 09:40:09AM +0300, Canberk Koç wrote:
>> > Hello Andreas,
>> >
>> > Thanks for guiding a lot. I'll take this package as a reference to my
>> work
>> > i think.
>>
>> Fine.
>>
>> > For this package test uses all of data but i look it again if
>> > there is unnecessary data in examples i'll erase it.
>>
>> Please do so.  The problem is that at build time the same tests are
>> running and leave a lot of result files (*.tmp files etc) inside the
>> test directory.  You are installing these all into the binary package
>> for no good reason.  I suggest you clean up the test dir first and copy
>> afterwards.  May be the easiest way is to use the clean target of
>> test/Makefile.  In any case the file structure of the example package
>> should not contain any other files than the plain source.
>>
>> > In problem matter svn
>> > have tmp dirs and git doesn't tests uses them i think .
>>
>> Well, I think Git ignores empty directories.  That's no harm since at
>> build time the original tarball is used anyway.  The directories you
>> are mentioning are all empty if I'm not misleaded.
>>
>> Will you manage to clean up the example directory tree and also the path
>> to perl interpreter until today evening?  If not please ask for help to
>> let me know that there might be some stumbling stones.
>>
>> Kind regards
>>
>>Andreas.
>>
>> --
>> http://fam-tille.de
>>
>>

Re: request for sponsorship: r-cran-r.cache r-cran-future r-cran-globals r-cran-listev r-bioc-dnacopy

2016-06-26 Thread Andreas Tille 
On Sun, Jun 26, 2016 at 04:03:28PM -0400, Michael Crusoe wrote:
> > Needs r-cran-pscbs.
> 
> Whoops, forgot to push that -- r-cran-scbs is reading for review as well.

Yup, but we also need to wait for Build-Depends ...

> > Thanks for your work on this
> 
> Thank you for your review.

You are welcome

  Andreas.

-- 
http://fam-tille.de

Re: request for sponsorship: r-cran-r.cache r-cran-future r-cran-globals r-cran-listev r-bioc-dnacopy

2016-06-26 Thread Michael Crusoe 
On Sun, Jun 26, 2016 at 3:30 PM, Andreas Tille  wrote:

> Hi Michael,
>
> On Sun, Jun 26, 2016 at 11:08:57AM -0400, Michael Crusoe wrote:
> >
> > Good catch; I've updated r-cran-r.cache, r-cran-future, r-cran-globals,
> and
> > r-cran-listenv.
>
> Uploaded with exception of r-cran-future which Build-Depends
> r-cran-globals and r-cran-listenv.  I tend to wait with uploads to new
> until all preconditions are available in unstable.


Thanks!


>
> > cnvkit is now available for review as well
>
> Needs r-cran-pscbs.
>

Whoops, forgot to push that -- r-cran-scbs is reading for review as well.


> Thanks for your work on this


Thank you for your review.


>
>  Andreas.
>
> --
> http://fam-tille.de
>
>


-- 
Michael R. Crusoe
Community Engineer & Co-founder
Common Workflow Language project
https://impactstory.org/u/-0002-2961-9670
michael.cru...@gmail.com
+32 (0) 2 808 25 58
+1 480 627 9108

Bug#828184: marked as done (ITP: r-cran-r.cache -- R package: Fast and Light-Weight Caching of Objects and Results)

2016-06-26 Thread Debian Bug Tracking System 
Your message dated Sun, 26 Jun 2016 20:00:49 +
with message-id 
and subject line Bug#828184: fixed in r-cran-r.cache 0.12.0-1
has caused the Debian Bug report #828184,
regarding ITP: r-cran-r.cache -- R package: Fast and Light-Weight Caching of 
Objects and Results
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
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-- 
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--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: r-cran-r.cache
  Version : 0.12.0
  Upstream Author : Henrik Bengtsson 
* URL : https://github.com/HenrikBengtsson/R.cache
* License : LGPL (>= 2.1)
  Programming Lang: R
  Description : R package: Fast and Light-Weight Caching of Objects and 
Results

Memoization can be used to speed up repetitive and computational expensive
function calls.  The first time a function that implements memoization is
called the results are stored in a cache memory.  The next time the function is
called with the same set of parameters, the results are momentarily retrieved
from the cache avoiding repeating the calculations.  With this package, any R
object can be cached in a key-value storage where the key can be an arbitrary
set of R objects.  The cache memory is persistent (on the file system).

Dependency of r-cran-pscbs, will be team maintained by the Debian Med team
--- End Message ---
--- Begin Message ---
Source: r-cran-r.cache
Source-Version: 0.12.0-1

We believe that the bug you reported is fixed in the latest version of
r-cran-r.cache, 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 828...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Michael R. Crusoe  (supplier of updated 
r-cran-r.cache package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
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Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Description:
 r-cran-r.cache - R package: Fast and Light-Weight Caching of Objects and 
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Closes: 828184
Changes:
 r-cran-r.cache (0.12.0-1) unstable; urgency=medium
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Bug#828194: marked as done (ITP: r-cran-listenv -- R package: Environments Behaving (Almost) as Lists)

2016-06-26 Thread Debian Bug Tracking System 
Your message dated Sun, 26 Jun 2016 20:00:48 +
with message-id 
and subject line Bug#828194: fixed in r-cran-listenv 0.6.0-1
has caused the Debian Bug report #828194,
regarding ITP: r-cran-listenv -- R package: Environments Behaving (Almost) as 
Lists
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
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-- 
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Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: r-cran-listenv
  Version : 0.6.0
  Upstream Author : Henrik Bengtsson 
* URL : https://github.com/HenrikBengtsson/listenv
* License : LGPL 2.1+
  Programming Lang: R
  Description : R package: Environments Behaving (Almost) as Lists

List environments are environments that have list-like properties. For
 instance, the elements of a list environment are ordered and can be accessed
 and iterated over using index subsetting, e.g. 'x <- listenv(a=1, b=2); for (i
 in seq_along(x)) x[[i]] <- x[[i]]^2; y <- as.list(x)'.

A dependency of r-cran-pscbs, will be team maintained by Debian Med.
--- End Message ---
--- Begin Message ---
Source: r-cran-listenv
Source-Version: 0.6.0-1

We believe that the bug you reported is fixed in the latest version of
r-cran-listenv, 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 828...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Michael R. Crusoe  (supplier of updated 
r-cran-listenv package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
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Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Description:
 r-cran-listenv - R package: Environments Behaving (Almost) as Lists
Closes: 828194
Changes:
 r-cran-listenv (0.6.0-1) unstable; urgency=medium
 .
   * Initial release. (Closes: #828194)
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Bug#828690: ITP: r-cran-pscbs -- R package: Analysis of Parent-Specific DNA Copy Numbers

2016-06-26 Thread Michael R. Crusoe 
Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: r-cran-pscbs
  Version : 0.61.0
  Upstream Author : Henrik Bengtsson 
* URL : https://github.com/HenrikBengtsson/PSCBS
* License : GPL-2+
  Programming Lang: R
  Description : R package: Analysis of Parent-Specific DNA Copy Numbers

Segmentation of allele-specific DNA copy number data and detection of regions
 with abnormal copy number within each parental chromosome. Both tumor-normal
 paired and tumoronly analyses are supported.

Prerequisite for cnvkit, to be maintained by Debian Med

Re: request for sponsorship: r-cran-r.cache r-cran-future r-cran-globals r-cran-listev r-bioc-dnacopy

2016-06-26 Thread Andreas Tille 
Hi Michael,

On Sun, Jun 26, 2016 at 11:08:57AM -0400, Michael Crusoe wrote:
> 
> Good catch; I've updated r-cran-r.cache, r-cran-future, r-cran-globals, and
> r-cran-listenv.

Uploaded with exception of r-cran-future which Build-Depends
r-cran-globals and r-cran-listenv.  I tend to wait with uploads to new
until all preconditions are available in unstable.
 
> cnvkit is now available for review as well

Needs r-cran-pscbs.
 
Thanks for your work on this

 Andreas.

-- 
http://fam-tille.de

Re: BWA

2016-06-26 Thread Andreas Tille 
Hi Canberk

On Sat, Jun 25, 2016 at 11:43:07PM +0300, Canberk Koç wrote:
> I upload autopkgtest to git for bwa. Thanks for your help.

Just to confirm that I uploaded t-coffee and bwa (waiting for your fixes
for primer3).

Kind regards

   Andreas.

-- 
http://fam-tille.de

Re: Primer3

2016-06-26 Thread Canberk Koç 
Hello Andreas,

I must go to hospital due to  an emergency situation. Now i'll look for
clean up these files.

Best Regards

Canberk Koç
www.about.me/canberkkoc
26 Haz 2016 15:12 tarihinde "Andreas Tille"  yazdı:

> On Sun, Jun 26, 2016 at 09:40:09AM +0300, Canberk Koç wrote:
> > Hello Andreas,
> >
> > Thanks for guiding a lot. I'll take this package as a reference to my
> work
> > i think.
>
> Fine.
>
> > For this package test uses all of data but i look it again if
> > there is unnecessary data in examples i'll erase it.
>
> Please do so.  The problem is that at build time the same tests are
> running and leave a lot of result files (*.tmp files etc) inside the
> test directory.  You are installing these all into the binary package
> for no good reason.  I suggest you clean up the test dir first and copy
> afterwards.  May be the easiest way is to use the clean target of
> test/Makefile.  In any case the file structure of the example package
> should not contain any other files than the plain source.
>
> > In problem matter svn
> > have tmp dirs and git doesn't tests uses them i think .
>
> Well, I think Git ignores empty directories.  That's no harm since at
> build time the original tarball is used anyway.  The directories you
> are mentioning are all empty if I'm not misleaded.
>
> Will you manage to clean up the example directory tree and also the path
> to perl interpreter until today evening?  If not please ask for help to
> let me know that there might be some stumbling stones.
>
> Kind regards
>
>Andreas.
>
> --
> http://fam-tille.de
>
>

Re: request for sponsorship: r-cran-r.cache r-cran-future r-cran-globals r-cran-listev r-bioc-dnacopy

2016-06-26 Thread Michael Crusoe 
Hey Andreas,

Hello from the Galaxy Community Conference in Bloomington, Indiana, USA.

Good catch; I've updated r-cran-r.cache, r-cran-future, r-cran-globals, and
r-cran-listenv.

cnvkit is now available for review as well



On Sun, Jun 26, 2016 at 2:15 AM, Andreas Tille  wrote:

> Hi Michael,
>
> I started with r-bioc-dnacopy and noticed that you can easily add an
> autopkgtest.  I have not checked the other ones since I'll be AFK now
> for some hours.  Please verify whether you can add some tests to the
> other r-* packages since we try to get as much as possible tested.
>
> I'll sponsor later if nobody else will beat me.
>
> Kind regards
>
>  Andreas.
>
> On Sat, Jun 25, 2016 at 09:50:13PM -0400, Michael Crusoe wrote:
> > These are all dependencies of cnvkit http://cnvkit.readthedocs.io/
>
> --
> http://fam-tille.de
>
>


-- 
Michael R. Crusoe
Community Engineer & Co-founder
Common Workflow Language project
https://impactstory.org/u/-0002-2961-9670
michael.cru...@gmail.com
+32 (0) 2 808 25 58
+1 480 627 9108

Re: Primer3

2016-06-26 Thread Andreas Tille 
On Sun, Jun 26, 2016 at 09:40:09AM +0300, Canberk Koç wrote:
> Hello Andreas,
> 
> Thanks for guiding a lot. I'll take this package as a reference to my work
> i think.

Fine.

> For this package test uses all of data but i look it again if
> there is unnecessary data in examples i'll erase it.

Please do so.  The problem is that at build time the same tests are
running and leave a lot of result files (*.tmp files etc) inside the
test directory.  You are installing these all into the binary package
for no good reason.  I suggest you clean up the test dir first and copy
afterwards.  May be the easiest way is to use the clean target of
test/Makefile.  In any case the file structure of the example package
should not contain any other files than the plain source.

> In problem matter svn
> have tmp dirs and git doesn't tests uses them i think .

Well, I think Git ignores empty directories.  That's no harm since at
build time the original tarball is used anyway.  The directories you
are mentioning are all empty if I'm not misleaded.
 
Will you manage to clean up the example directory tree and also the path
to perl interpreter until today evening?  If not please ask for help to
let me know that there might be some stumbling stones.

Kind regards

   Andreas.

-- 
http://fam-tille.de

Re: request for sponsorship: r-cran-r.cache r-cran-future r-cran-globals r-cran-listev r-bioc-dnacopy

2016-06-26 Thread Andreas Tille 
Hi Michael,

I started with r-bioc-dnacopy and noticed that you can easily add an
autopkgtest.  I have not checked the other ones since I'll be AFK now
for some hours.  Please verify whether you can add some tests to the
other r-* packages since we try to get as much as possible tested.

I'll sponsor later if nobody else will beat me.

Kind regards

 Andreas.

On Sat, Jun 25, 2016 at 09:50:13PM -0400, Michael Crusoe wrote:
> These are all dependencies of cnvkit http://cnvkit.readthedocs.io/

-- 
http://fam-tille.de

Re: Primer3

2016-06-26 Thread Andreas Tille 
Hi Canberk,

On Sun, Jun 26, 2016 at 06:43:27AM +0300, Canberk Koç wrote:
> Hi Andreas,
> 
> I upload Primer3 changes to git. But there is a problem svn and git
> packages have differences it might be a problem . Thanks for your help.

Could you please specify what exact problems there might be?

Moreover, if you build the package you get lintian warnings that should
be easy to fix.  The simplest way to verify this if you create a
.lintianrc file like:

$ cat ~/.lintianrc 
color=always
display-experimental=no
display-info=yes
pedantic=no
## show-overrides=yes

and than run lintian on the resulting changes file.  Please fix those
issues like:

$ cat ~/.lintianrc 
color=always
display-experimental=no
display-info=yes
pedantic=no
## show-overrides=yes


BTW, you created a certain scheme how to move examples around.  Do you
know dh_installexamples(1) and that it is sufficient to simply add the
files in question to debian/.examples ?

While in this case you surely need an override_dh_installexamples to fix
the lintian issues by using sed to fix the interpreter to reach the
status you had previously commited to Git it would have been perfectly
sufficient if you had added the dirs in question to primer3.examples.

Finally installing everything in the test dirs *after* the tests were
run leaves a lot of temporary data inside the dirs which end up inside
the resulting package which should not be.  Either you clean up this in
a override_dh_auto_test or you be a bit more cautiously when copying the
files.

Since the test data are consuming a severe amount of architecture all
type files in the resulting package it is better to move them into a
separate architecture all binary package.  I guess you are not that
comfortable with the packaging skills and thus I just did the change.
Please make sure you understand my commit and in future try to do the
same if you get the according lintian warning.

In short the following is what I want you to do:  Understand, that
example data are now in primer3-examples, fix the interpreter lines via
sed statements and remove temporary test data that are not needed inside
the resulting package.

Kind regards

   Andreas.

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