Bug#871660: ITP: fairsim -- ImageJ plugin for SIM reconstruction

2017-09-28 Thread Carnë Draug 
On 10 August 2017 at 15:28, Yanhao Mo <yanha...@gmail.com> wrote:
> Maybe your name listed at the Owner field using wrong encoding. because
> it's showing "=?utf-8?q?Carn=C3=AB_Draug?=". Is it correct?

It is not.  The name should be Carnë Draug.  It was automatically picked
by reportbug from DEBFULLNAME though.  Not sure if it's a bug somewhere.

Carnë

Bug#876374: ITP: libdist-zilla-plugin-modulebuildtiny-fallback-perl -- Dist::Zilla plugin that generates a Build.PL with fallback on Module::Build

2017-09-21 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: Carnë Draug <carandraug+...@gmail.com>

* Package name: libdist-zilla-plugin-modulebuildtiny-fallback-perl
  Version : 0.025
  Upstream Author : Karen Etheridge <et...@cpan.org>
* URL : 
https://metacpan.org/release/Dist-Zilla-Plugin-ModuleBuildTiny-Fallback
* License : perl 5
  Programming Lang: Perl
  Description : Dist::Zilla plugin that generates a Build.PL with fallback 
on Module::Build

 Dist::Zilla::Plugin::ModuleBuildTiny::Fallback is a Dist::Zilla
 plugin that provides a Build.PL in your distribution that attempts to
 use Module::Build::Tiny when available, falling back to Module::Build
 when it is missing and printing a warning about it.
 .
 This is useful when your distribution is installing on an older perl
 (before approximately 5.10.1) with a toolchain that has not been
 updated, where configure_requires metadata is not understood and
 respected -- or where Build.PL is being run manually without the user
 having read and understood the contents of META.yml or META.json.

Bug#876292: ITP: libdist-zilla-plugin-makemaker-fallback-perl -- Dist::Zilla plugin that generates a Makefile.PL with deprecation warnings

2017-09-20 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: = Carnë Draug <carandraug+...@gmail.com>

* Package name: libdist-zilla-plugin-makemaker-fallback-perl
  Version : 0.023
  Upstream Author : Karen Etheridge <et...@cpan.org>
* URL : 
https://metacpan.org/release/Dist-Zilla-Plugin-MakeMaker-Fallback
* License : perl 5
  Programming Lang: Perl
  Description : Dist::Zilla plugin that generates a Makefile.PL with 
deprecation warnings

 Dist::Zilla::Plugin::MakerMaker::Fallback is a Dist::Zilla plugin
 that will generate a Makefile.PL as fallback to a Build.PL.  The
 Makefile.PL will issue a warning about using a legacy toolchain,
 since modern tools will default to Build.PL.

Bug#876289: ITP: libdist-zilla-plugin-makemaker-awesome-perl -- Dist::Zilla plugin with more options than [MakeMaker]

2017-09-20 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: Carnë Draug <carandraug+...@gmail.com>

* Package name: libdist-zilla-plugin-makemaker-awesome-perl
  Version : 0.38
  Upstream Author : Karen Etheridge <et...@cpan.org>
* URL : 
https://metacpan.org/release/Dist-Zilla-Plugin-MakeMaker-Awesome
* License : perl 5
  Programming Lang: Perl
  Description : Dist::Zilla plugin with more options than [MakeMaker]

 Dist::Zilla::Plugin::MakeMaker::Awesome is a Dist::Zilla plugin that
 generates a Makefile.PL making use of ExtUtils::MakeMaker.  It is
 similar to the Dist::Zilla::Plugin::MakeMaker, and is actually a
 subclass of it, but provides several options to run custom code on
 the generated Makefile.PL.

Bug#876287: ITP: libdist-zilla-plugin-modulebuildtiny-perl -- Dist::Zilla plugin to create a Build.PL that uses Module::Build::Tiny

2017-09-20 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: Carnë Draug <carandraug+...@gmail.com>

* Package name: libdist-zilla-plugin-modulebuildtiny-perl
  Version : 0.015
  Upstream Author : Leon Timmermans <faw...@gmail.com>
* URL : 
https://metacpan.org/release/Dist-Zilla-Plugin-ModuleBuildTiny
* License : perl 5
  Programming Lang: Perl
  Description : Dist::Zilla plugin to create a Build.PL that uses 
Module::Build::Tiny

Dist::Zilla::Plugin::ModuleBuildTiny is a Dist::Zilla plugin to create
a Build.PL file that makes use of Module::Build::Tiny.  It provides an
alternative to Dist::Zilla::Plugin::ModuleBuild which would create a
Build.PL files that makes use of Module::Build as the underlying build
system.

Bug#876273: ITP: libdist-zilla-plugin-checkbin-perl -- Dist::Zilla plugin for checking command at build time

2017-09-20 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: Carnë Draug <carandraug+...@gmail.com>

* Package name: libdist-zilla-plugin-checkbin-perl
  Version : 0.007
  Upstream Author : Karen Etheridge <et...@cpan.org>
* URL : https://metacpan.org/release/Dist-Zilla-Plugin-CheckBin
* License : Perl_5
  Programming Lang: Perl
  Description : Dist::Zilla plugin for checking command at build time

Dist::Zilla::Plugin::CheckBin is a Dist::Zilla plugin that modifies
the Makefile.PL or Build.PL in your distribution to contain a
Devel::CheckBin call, that asserts that a particular command is
available. If it is not available, the program exits with a status of
zero, which on a CPAN Testers machine will result in a NA result.

Bug#655420: ITP: jtransforms -- A multithreaded FFT library written in pure Java

2017-08-21 Thread Carnë Draug 
On 20 August 2017 at 17:57, Ghislain Vaillant  wrote:
> On 20/08/17 15:25, Andreas Tille wrote:>
>>
>> please consider packaging this in either Debian Science or pkg-java
>> team.
>
>
> I'd recommend the Java Team for this one and read Markus' tutorial for maven
> [1] before debianizing. The source package should be named
> libjtransforms-java.
>
> [1]
> http://collab.debian.net/portal/planet-debian/markus-koschany-pdfsam-how-to-upgrade-a-maven-application-for-debian
>
> Ghis

Hi everyone

I have already packaged it for pkg-java team.  See
https://github.com/carandraug/debian-libjtransforms-java

If you want to try it, it is dependent on JLargeArrays which I have
also packaged.  See
https://github.com/carandraug/debian-libjlargearrays-java

I am packaging this because they are dependencies of fairsim [2] which
I have already started to package.

None of these are uploaded because pkg-java team prefers I finish
packaging fairsim first and then upload all three at same time.

Carnë

[2] http://fairsim.github.io/

Bug#871660: ITP: fairsim -- ImageJ plugin for SIM reconstruction

2017-08-10 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: =?utf-8?q?Carn=C3=AB_Draug?= 

* Package name: fairsim
  Version : 1.2.0
  Upstream Author : Marcel Müller 
* URL : https://fairsim.github.io/
* License : GPL-2+
  Programming Lang: Java
  Description : ImageJ plugin for SIM reconstruction

Structured Illumination Microscopy (SIM) is a super resolution
microscopy technique.  Widefield images with varying illumination
patterns are acquired and then reconstructed with increased
spatial resolution.  fairSIM implements the reconstruction
algorithm by Gustaffson and Heintzmann.

Bug#655420: ITP: jtransforms -- A multithreaded FFT library written in pure Java

2017-08-03 Thread Carnë Draug 
Package: wnpp
Followup-For: Bug #655420
Owner: =?utf-8?q?Carn=C3=AB_Draug?=

Bug#868330: ITP: libalgorithm-svm-perl -- bindings for the libsvm Support Vector Machine library

2017-07-14 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: =?utf-8?q?Carn=C3=AB_Draug?= 

* Package name: libalgorithm-svm-perl
  Version : 0.13
  Upstream Author : Matthew Laird 
* URL : https://metacpan.org/release/Algorithm-SVM
* License : Artistic or GPL-1+
  Programming Lang: Perl
  Description : bindings for the libsvm Support Vector Machine library

 Algorithm::SVM implements a Support Vector Machine for Perl. Support Vector
 Machines provide a method for creating classifcation functions from a set of
 labeled training data, from which predictions can be made for subsequent data
 sets.

This is package is mainly abandoned upstream but is a dependency
(currently vendorized) of psortb for debian-med.

Bug#867920: ITP: libjlargearrays-java -- Java library for one dimensional arrays up to 2^63 elements

2017-07-10 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: =?utf-8?q?Carn=C3=AB_Draug?= 

* Package name: libjlargearrays-java
  Version : 1.6
  Upstream Author : Piotr Wendykier 
* URL : https://gitlab.com/ICM-VisLab/JLargeArrays
* License : BSD-2-Clause
  Programming Lang: Java
  Description : Java library for one dimensional arrays up to 2^63 elements

Current implementations of Java Virtual Machines allow the creation of
one-dimensional arrays of length smaller than 2^31 elements.
JLargeArrays addresses the problem of maximal size of one-dimensional
Java arrays providing classes that can store up to 2^63 primitive
elements.

JLargeArrays provides the abstract class for primitive types, as well
as the non abstract classes for Number classes, String, bit values,
complex numbers, and objects.  It also supports subarrays.

This package is a common dependency on scientific java software where
the 2^31 number of elements is a common issue.

Bug#866748: ITP: libome-common -- C++ library providing common functionality to other OME C++ projects

2017-07-01 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: Carnë Draug <carandraug+...@gmail.com>

* Package name: libome-common
  Version : 5.4.0
  Upstream Author : Open Microscopy Environment 
<ome-us...@lists.openmicroscopy.org.uk>
* URL : https://www.openmicroscopy.org/site/products/ome-files-cpp
* License : BSD-2-Clause
  Programming Lang: C++
  Description : C++ library providing common and portability functionality 
for all OME C++ components

OME Common is a standalone C++ library required by other OME C++
projects for common functionality which is not readily available from
the C++ Standard Library.  This includes basic portability functions,
to wrapping other libraries to make them usable with Modern C++
programming practices.

It serves a similar purpose to the OME formats-common Java library,
with some shared functionality, though for the most part they are
quite different.

---

This package is a basic dependency for ome-files, the C++ implementation
of a writer of the OME model.

I plan to maintain it as part of my day to day job.  I believe that
the debian-med packaging team to be a goof fit though as the follow
up on this package is the rest of the ome packages, starting with
ome-files, then bioformats, then omero to provide a complete suite
for management of biological microscopy data.

Bug#862352: RFP: libsystem-info-perl -- package·to·obtain·basic·system·information

2017-05-11 Thread Carnë Draug 
Package: wnpp
Severity: wishlist

* Package name: libsystem-info-perl
  Version : 0.054
  Upstream Author : H.Merijn·Brand·
* URL : https://metacpan.org/release/System-Info
* License : Artistic·or·GPL-1+
  Programming Lang: Perl
  Description : package·to·obtain·basic·system·information

System::Info·tries·to·present·system-related·information,·like·number   


of·CPUs,·architecture,·OS,·and·release·related·information·in·a 


system-independent·way.··This·releases·the·user·of·thos·module·of·the   


need·to·know·if·the·information·comes·from·Windows,·Linux,·HP-UX,   


AIX,·Solaris,·Irix,·or·VMS,·and·if·the·architecture·is·i386,·x64,   


pa-risc2,·or·arm.

Bug#853983: ITP: libdist-zilla-role-pluginbundle-pluginremover-perl -- Dist::Zilla plugin to add '-remove' functionality to a bundle

2017-02-02 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: =?utf-8?q?Carn=C3=AB_Draug?= 

* Package name: libdist-zilla-role-pluginbundle-pluginremover-perl
  Version : 0.104
  Upstream Author : Randy Stauner 
* URL : 
https://metacpan.org/release/Dist-Zilla-Role-PluginBundle-PluginRemover
* License : Artistics or GPL-1+
  Programming Lang: Perl
  Description : Dist::Zilla plugin to add '-remove' functionality to a 
bundle

Dist::Zilla::Role::PluginBundle::PluginRemover enables Dist::Zilla
plugin bundles to automatically remove any plugins specified by the
-remove attribute.  This is similar to the @Filter plugin but with
less typing.

Bug#853982: ITP: libconfig-mvp-slicer-perl -- Extract embedded plugin config from parent config

2017-02-02 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: =?utf-8?q?Carn=C3=AB_Draug?= 

* Package name: libconfig-mvp-slicer-perl
  Version : 0.302
  Upstream Author : Randy Stauner 
* URL : https://metacpan.org/release/Config-MVP-Slicer
* License : Artistic or GPL-1+
  Programming Lang: Perl
  Description : Extract embedded plugin config from parent config

Config::MVP::Slicer can be used to extract embedded configurations
for other plugins out of larger (parent) configurations.  An example
where this can be useful is plugin bundles (see
Config::MVP::Assembler::WithBundles).  A bundle loads other plugins
with a default configuration that works most of the time, but
sometimes you wish you could customize the configuration for one of
those plugins without having to remove the plugin from the bundle and
re-specify it separately.

Bug#853229: ITP: libdist-zilla-plugin-readmefrompod-perl -- Dist::Zilla plugin to generate a README from Pod

2017-01-30 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: =?utf-8?q?Carn=C3=AB_Draug?= 

* Package name: libdist-zilla-plugin-readmefrompod-perl
  Version : 0.35
  Upstream Author : Fayland Lam 
* URL : https://metacpan.org/release/Dist-Zilla-Plugin-ReadmeFromPod
* License : Artistic or GPL-1+
  Programming Lang: Perl
  Description : Dist::Zilla plugin to generate a README from Pod

Dist::Zilla::Plugin::ReadmeFromPod is a Dist::Zilla plugin that
generates a README from a specific module using Pod::Readme.  It
supports the conversion to "html", "pod", "markdown" and "rtf"
formats.

Bug#853217: ITP: libpod-weaver-section-legal-complicated-perl -- Pod::Weaver plugin for Pod sections of authors, copyright holders, and licenses

2017-01-30 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: =?utf-8?q?Carn=C3=AB_Draug?= <carandraug+...@gmail.com>

* Package name: libpod-weaver-section-legal-complicated-perl
  Version : 1.21
  Upstream Author : Carnë Draug <cdr...@cpan.org>
* URL : 
https://metacpan.org/release/Pod-Weaver-Section-Legal-Complicated
* License : GPL-3+
  Programming Lang: Perl
  Description : Pod::Weaver plugin for Pod sections of authors, copyright 
holders, and licenses

Pod::Weaver::Section::Legal::Complicated is a Pod::Weaver plugin to
create Pod sections listing authors, copyright owners, and licenses
of each module in the distribution.  It is targeted at distributions
with a large number of modules and where different module may have
different authos, copyright holders, and licenses.  It does so by
parsing individual modules and looking for specific comments.

Bug#853215: ITP: libpod-weaver-section-contributors-perl -- Pod::Weaver plugin for a section listing contributors

2017-01-30 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: =?utf-8?q?Carn=C3=AB_Draug?= 

* Package name: libpod-weaver-section-contributors-perl
  Version : 0.009
  Upstream Author : Keedi Kim 
* URL : https://metacpan.org/release/Pod-Weaver-Section-Contributors
* License : Artistic or GPL-1+
  Programming Lang: Perl
  Description : Pod::Weaver plugin for a section listing contributors

Pod::Weaver::Section::Contributors provides a Pod::Weaver plugin to
generate a section listing modules contributors.  These can be named
on the source of individual modules as well as on the pod weaver and
dist zilla configuration files.

Bug#853212: ITP: libpod-weaver-plugin-ensureuniquesections-perl -- Pod::Weaver plugin to check for duplicate Pod section headers

2017-01-30 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: =?utf-8?q?Carn=C3=AB_Draug?= 

* Package name: libpod-weaver-plugin-ensureuniquesections-perl
  Version : 0.163250
  Upstream Author : Ryan C. Thompson 
* URL : 
https://metacpan.org/release/Pod-Weaver-Plugin-EnsureUniqueSections
* License : Artistic or GPL-1+
  Programming Lang: Perl
  Description : Pod::Weaver plugin to check for duplicate Pod section 
headers

Pod::Weaver::Plugin::EnsureUniqueSections is a Pod::Weaver plugin to
ensure that the Pod after weaving has no duplicate top-level section
headers.  This can help you if you are converting from writing all
your own POD to generating it with Pod::Weaver.  If you begin
generating a section with Pod::Weaver but you forget to delete the
manually written section of the same name, this plugin will warn you.

Bug#853190: ITP: libpod-elemental-transformer-list-perl -- Pod transformer to convert :lists sections to standard Pod lists

2017-01-30 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: =?utf-8?q?Carn=C3=AB_Draug?= 

* Package name: libpod-elemental-transformer-list-perl
  Version : 0.102000
  Upstream Author : Ricardo SIGNES 
* URL : https://metacpan.org/release/Pod-Elemental-Transformer-List
* License : Artistic or GPL-1+
  Programming Lang: Perl
  Description : Pod transformer to convert :lists sections to standard Pod 
lists

Pod::Elemental::Transformer::List is a transformer for a
Pod::Elemental::Document which produces traditional Pod5 lists
(=over / =item / =item / =back) from an alternative more compact
syntax.

Bug#853191: ITP: libpod-weaver-section-generatesection-perl -- Pod::Weaver plugin

2017-01-30 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: =?utf-8?q?Carn=C3=AB_Draug?= <carandraug+...@gmail.com>

* Package name: libpod-weaver-section-generatesection-perl
  Version : 1.02
  Upstream Author : Carnë Draug <carandraug+...@gmail.com>
* URL : 
https://metacpan.org/release/Pod-Weaver-Section-GenerateSection
* License : GPL-3+
  Programming Lang: Perl
  Description : Pod::Weaver plugin to add Pod sections from a template text.

Pod::Weaver::Section::GenerateSection provides a Pod::Weaver plugin
to introduce a Pod section in the distribution modules.  This section
is generated from a template text where multiple variables can be
expanded to the values in the distribution metadata.

Bug#852810: ITP: libdist-zilla-plugin-autometaresources-perl -- Dist::Zilla plugin to reduce MetaResources

2017-01-27 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: =?utf-8?q?Carn=C3=AB_Draug?= 

* Package name: libdist-zilla-plugin-autometaresources-perl
  Version : 1.21
  Upstream Author : Alex J. G. Burzyński 
* URL : 
https://metacpan.org/release/Dist-Zilla-Plugin-AutoMetaResources
* License : Artistic or GPL-1+
  Programming Lang: Perl
  Description : Dist::Zilla plugin to reduce duplication on MetaResources

Dist::Zilla::Plugin::AutoMetaResources is a Dist::Zilla MetaProvider
plugin that simplifies the addition of bugtracker and repository
"resources" to the distribution metadata.

Bug#852004: RFP for bioperl's Bio-EUtilities

2017-01-27 Thread Carnë Draug 
On 27 January 2017 at 12:03, Andreas Tille  wrote:
> [dropped debian-perl list from CC]
>
> Hi Carnė,
>
> On Thu, Jan 26, 2017 at 06:12:41PM +, Carnė Draug wrote:
>> I have attached a git patch which adds a quilt patch to the repos.
>> This change inlines the DTDs in the xml files and pdebuild now
>> succeeds.
>>
>> If this change fixes it for debian, we can apply it upstream.
>
> The package builds with this patch and I have commited it to Git.
>
> Please note also commit 164117cc7c49036cf19dbab04e75f8e83db2dbdd which
> fixes the spelling of some text I've copied from your description.
>
> Please let me know whether I should wait for you fixing this upstream or
> whether I should upload with the current patch.
>

Please upload with the current patch.  We are currently fixing this
upstream [1] but it might take a while.  The reason is that while
fixing this we noticed there is no code to reproduce the xml files
used in the test suite (they are saved queries to e-utils).  I would
rather fix the whole issue with a script that downloads new xml and
inlines the DTDs than further distancing the xml in the repos from the
real e-utils replies.

> Thanks for your helpful contribution (I admit its not clear to me
> why you initially said you are not comfortable with the Debian
> packaging - providing a quilt patch is somehow quite close to
> beeing able to maintain the package ;-) )
>

When I wrote the email I wasn't comfortable.  I then spent all week at
work setting up my system and learning the Debian maintainer tools
with help from the pkg-perl team.

Carnë

[1] https://github.com/bioperl/Bio-EUtilities/issues/6

Bug#852797: ITP: libtest-mojibake-perl -- module to check source for encoding misbehavior

2017-01-27 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: =?utf-8?q?Carn=C3=AB_Draug?= 

* Package name: libtest-mojibake-perl
  Version : 1.1
  Upstream Author : Stanislaw Pusep 
* URL : https://metacpan.org/release/Test-Mojibake
* License : Artistic or GPL-1+
  Programming Lang: Perl
  Description : module to check source for encoding misbehavior

Many modern text editors automatically save files using UTF-8
encoding, however, perl interpreter does not expects it by default.
Whereas this does not represent a big deal on (most) backend-oriented
programs, Web framework (Catalyst, Mojolicious) based applications
will suffer of so-called Mojibake (lit. "unintelligible sequence of
characters").

Test::Mojibake lets you check for inconsistencies in source and
documentation encoding, and report its results in a standard
Test::Simple fashion.

Bug#852795: ITP: libdist-zilla-plugin-mojibaketests-perl -- Dist::Zilla plugin that provides author tests for source encoding

2017-01-27 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: =?utf-8?q?Carn=C3=AB_Draug?= 

* Package name: libdist-zilla-plugin-mojibaketests-perl
  Version : 0.8
  Upstream Author : Stanislaw Pusep 
* URL : https://metacpan.org/release/Dist-Zilla-Plugin-MojibakeTests
* License : Artistic or GPL+1
  Programming Lang: Perl
  Description : Dist::Zilla plugin that provides author tests for source 
encoding

Dist::Zilla::Plugin::MojibakeTests is a Dist::Zilla plugin that
provides a standard Test::Mojibake author test which checks for
inconsistencies in source and documentation encoding.

Bug#852004: RFP for bioperl's Bio-EUtilities

2017-01-26 Thread Carnë Draug 
I have attached a git patch which adds a quilt patch to the repos.
This change inlines the DTDs in the xml files and pdebuild now
succeeds.

If this change fixes it for debian, we can apply it upstream.

Carnë
From 38a2038d0da47f6ac6b853b20b2934260257381d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Carn=C3=AB=20Draug?= 
Date: Thu, 26 Jan 2017 18:01:49 +
Subject: [PATCH] Inline DTDs on XML files required for testsuite so no
 internet is necessary

---
 debian/patches/inline-DTDs-on-testsuite | 948 
 debian/patches/series   |   1 +
 2 files changed, 949 insertions(+)
 create mode 100644 debian/patches/inline-DTDs-on-testsuite
 create mode 100644 debian/patches/series

diff --git a/debian/patches/inline-DTDs-on-testsuite b/debian/patches/inline-DTDs-on-testsuite
new file mode 100644
index 000..589c51c
--- /dev/null
+++ b/debian/patches/inline-DTDs-on-testsuite
@@ -0,0 +1,948 @@
+Index: libbio-eutilities-perl/t/data/eutils/egquery.xml
+===
+--- libbio-eutilities-perl.orig/t/data/eutils/egquery.xml
 libbio-eutilities-perl/t/data/eutils/egquery.xml
+@@ -1,11 +1,21 @@
+-
+-http://www.ncbi.nlm.nih.gov/entrez/query/DTD/egquery.dtd;>
+-
++
++
++
++
++
++
++
++
++
++]>
+ 
+ 
+-
+ 
+ 
+ Notch AND Mus musculus
+Index: libbio-eutilities-perl/t/data/eutils/einfo.xml
+===
+--- libbio-eutilities-perl.orig/t/data/eutils/einfo.xml
 libbio-eutilities-perl/t/data/eutils/einfo.xml
+@@ -1,5 +1,35 @@
+-
+-http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd;>
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++]>
+ 
+ 
+ 	pubmed
+Index: libbio-eutilities-perl/t/data/eutils/einfo_dbs.xml
+===
+--- libbio-eutilities-perl.orig/t/data/eutils/einfo_dbs.xml
 libbio-eutilities-perl/t/data/eutils/einfo_dbs.xml
+@@ -1,5 +1,35 @@
+-
+-http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd;>
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++]>
+ 
+ 
+ 	pubmed
+Index: libbio-eutilities-perl/t/data/eutils/elink_acheck.xml
+===
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_acheck.xml
 libbio-eutilities-perl/t/data/eutils/elink_acheck.xml
+@@ -1,5 +1,34 @@
+-
+-http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd;>
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++]>
+ 
+ 
+ 	protein
+Index: libbio-eutilities-perl/t/data/eutils/elink_acheck_corr.xml
+===
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_acheck_corr.xml
 libbio-eutilities-perl/t/data/eutils/elink_acheck_corr.xml
+@@ -1,5 +1,34 @@
+-
+-http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd;>
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++]>
+ 
+ 
+ 	protein
+Index: libbio-eutilities-perl/t/data/eutils/elink_dball.xml
+===
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_dball.xml
 libbio-eutilities-perl/t/data/eutils/elink_dball.xml
+@@ -1,5 +1,34 @@
+-
+-http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd;>
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++]>
+ 
+ 
+ 	protein
+Index: libbio-eutilities-perl/t/data/eutils/elink_lcheck.xml
+===
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_lcheck.xml
 libbio-eutilities-perl/t/data/eutils/elink_lcheck.xml
+@@ -1,5 +1,34 @@
+-
+-http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd;>
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++]>
+ 
+ 
+ 	protein
+Index: libbio-eutilities-perl/t/data/eutils/elink_lcheck_corr.xml
+===
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_lcheck_corr.xml
 libbio-eutilities-perl/t/data/eutils/elink_lcheck_corr.xml
+@@ -1,5 +1,34 @@
+-
+-http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd;>
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++]>
+ 
+ 
+ 	protein
+Index: libbio-eutilities-perl/t/data/eutils/elink_llinks.xml
+===
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_llinks.xml
 libbio-eutilities-perl/t/data/eutils/elink_llinks.xml
+@@ -1,5 +1,34 @@
+-
+-http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd;>
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++]>
+ 
+ 
+ 	protein
+Index: libbio-eutilities-perl/t/data/eutils/elink_llinks_corr.xml

Bug#852004:

2017-01-26 Thread Carnë Draug 
On 23 January 2017 at 22:45, gregor herrmann  wrote:
> On Mon, 23 Jan 2017 22:45:24 +0100, Andreas Tille wrote:
>
>> > The first is from a missing dependency (Bio::ASN1::EntrezGene),
>> > which is really optional (the comp test should skip that
>> > directory). The other is from XML::Simple, which is unusual; I’m
>> > wondering whether the underlying XML parser is checking the XML
>> > schema for the test reports. Any idea what the specific XML::SAX
>> > backend parser module used was?
>>
>> Sorry, I've sended a wrong version of the log with missing
>> Build-Depends.  Please check again.
>
> The tests fail for me as well, in a chroot with networking firewalled
> off.
>
> The errors are slightly different, probably because I have http_proxy
> set:
>
> http error : Operation in progress
> XML::Simple called at 
> /build/libbio-eutilities-perl-1.75/blib/lib/Bio/Tools/EUtilities.pm line 140.
> # Looks like your test exited with 255 before it could output anything.
> t/egquery.t .
> 1..18
> Dubious, test returned 255 (wstat 65280, 0xff00)
> Failed 18/18 subtests
>
> etc. for all t/e*.t tests
>
> /*
> With http_proxy unset I get:
>
> http error : Unknown IO error
> http error : connection refused
> XML::Simple called at 
> /build/libbio-eutilities-perl-1.75/blib/lib/Bio/Tools/EUtilities.pm line 140.
> # Looks like your test exited with 255 before it could output anything.
> t/egquery.t .
> 1..18
> Dubious, test returned 255 (wstat 65280, 0xff00)
> Failed 18/18 subtests
>
> */
>
> Anyway, it's quite clear that the tests try to access the internet
> which is forbidden by Debian policy (regardless of the fact if the
> fail gracefully or not), so they have to be skipped.
>
> [...]
> Of course an upstream fix, e.g. skipping tests if
> $ENV{NETWORK_TESTING} is not set etc., would be nicer.

I have managed to replicate the issue and found that it indeed comes
from XML::Simple (which Bio::EUtilities uses to parse the cml files)
and because it tries to connect to www.ncbi.nlm.nih.gov where the DTD
is.  I setup pbuilder with a hook to drop me on the chroot where the
tests were failing to investigate as described.

The only change I did was installing iptables (I guess there must
another way to block connections but I don't know how)

Everything works fine at the start in the chroot:

# iptables -L
Chain INPUT (policy ACCEPT)
target prot opt source   destination

Chain FORWARD (policy ACCEPT)
target prot opt source   destination

Chain OUTPUT (policy ACCEPT)
target prot opt source   destination
# perl -MXML::Simple -e 'XMLin("t/data/eutils/egquery.xml"); print
"hello\n"'
hello
# perl -Ilib -I. t/egquery.t
1..18
[...]

After blocking connections to www.ncbi.nlm.nih.gov, things fail:

# iptables -A INPUT -s 130.14.29.110 -j DROP
# perl -MXML::Simple -e 'XMLin("t/data/eutils/egquery.xml"); print
"hello\n"'
http error : Operation in progress
http error : unreachable network
XML::Simple called at -e line 1.
# perl -Ilib -I. t/egquery.t
1..18
http error : Operation in progress
http error : unreachable network
XML::Simple called at lib/Bio/Tools/EUtilities.pm line 140.
# Looks like your test exited with 255 before it could output anything.

And dropping the iptables rule rescues the behaviour:

# perl -MXML::Simple -e 'XMLin("t/data/eutils/egquery.xml"); print
"hello\n"'
hello
# perl -Ilib -I. t/egquery.t
1..18
ok 1 - get_db
[...]

Blocking the connection but removing the DOCTYPE line from the xml
file also fixes it:

# iptables -A INPUT -s 130.14.29.110 -j DROP
# grep -n DOCTYPE t/data/eutils/egquery.xml
2:http://www.ncbi.nlm.nih.gov/entrez/query/DTD/egquery.dtd;>
# sed -ie '2d' t/data/eutils/egquery.xml
# perl -MXML::Simple -e 'XMLin("t/data/eutils/egquery.xml"); print
"hello\n"'
hello

As upstream I could inline the DTD to avoid this.  I would prefer to
avoid have them as author only tests since that would cause them to be
skipped by CPAN testers.  Any opinions?

Carnë

Bug#852618: ITP: libdist-zilla-plugin-test-compile-perl -- common tests to check syntax of your modules, using only core modules

2017-01-25 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: =?utf-8?q?Carn=C3=AB_Draug?= 

* Package name: libdist-zilla-plugin-test-compile-perl
  Version : 2.056
  Upstream Author : Karen Etheridge 
* URL : https://metacpan.org/release/Dist-Zilla-Plugin-Test-Compile
* License : Artistic or GPL-1+
  Programming Lang: Perl
  Description : common tests to check syntax of your modules, using only 
core modules

Dist::Zilla::Plugin::Test::Compile is a Dist::Zilla plugin that runs
at the gather files (Dist::Zilla::Role::FileGatherer) stage, and
creates a test for correct perl file compilation only dependent on
core modules.

This test finds all modules and scripts in your distribution and try
to compile them one by one. This means it's a bit slower than loading
them all at once but it will catch more errors.

Bug#852467: ITP: libmoosex-types-email-perl -- Email address validation type constraints for Moose.

2017-01-24 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: =?utf-8?q?Carn=C3=AB_Draug?= 

* Package name: libmoosex-types-email-perl
  Version : 0.007
  Upstream Author : Tomas Doran (t0m)

Bug#852004: RFP for bioperl's Bio-EUtilities

2017-01-24 Thread Carnë Draug 
On 24 January 2017 at 07:26, Andreas Tille  wrote:
> Hi Gregor,
>
> On Mon, Jan 23, 2017 at 11:45:29PM +0100, gregor herrmann wrote:
>>
>> The tests fail for me as well, in a chroot with networking firewalled
>> off.
>>
>> The errors are slightly different, probably because I have http_proxy
>> set:
>>
>> http error : Operation in progress
>> XML::Simple called at 
>> /build/libbio-eutilities-perl-1.75/blib/lib/Bio/Tools/EUtilities.pm line 140.
>> # Looks like your test exited with 255 before it could output anything.
>> t/egquery.t .
>> 1..18
>> Dubious, test returned 255 (wstat 65280, 0xff00)
>> Failed 18/18 subtests
>>
>> etc. for all t/e*.t tests
>>
>> /*
>> With http_proxy unset I get:
>
> Thanks for verifying this.
>
>> Anyway, it's quite clear that the tests try to access the internet
>> which is forbidden by Debian policy (regardless of the fact if the
>> fail gracefully or not), so they have to be skipped.
>>
>> Andreas, you already know the trick with debian/tests/pkg-perl/smoke-skip
>> and using the file in debian/rules as well to disable tests during
>> build + autopkgtest. If you don't run okg-perl-autopkgtests, you can
>> use:
>
> Yes, I know.  I simply have forwarded the issue upstream since the RFP
> came from upstream and I considered it more sensible if they provide
> some means to exclude http access directly in their code.
>
>> Of course an upstream fix, e.g. skipping tests if
>> $ENV{NETWORK_TESTING} is not set etc., would be nicer.
>
> Exactly. :-)

I will fix this upstream.  I am learning what I can about debian
packaging at the moment (with pkg-perl) by trying to release some
packages that are needed by bioperl developers (bug #852467).  I am
hoping that allow me to follow this better.

>
>> (Hm, is this the package that was discussed on #debian-perl on IRC
>> earlier yesterday? :))
>
> May be - I'm usually not on IRC ...
>

Yes, this is that package.  I asked there about what was pkg-perl
preferred method to handle network tests [1].

Carnë

[1] https://lists.debian.org/debian-med/2017/01/msg00114.html

Bug#852004: RFP fpr bioperl's Bio-EUtilities

2017-01-23 Thread Carnë Draug 
On 23 January 2017 at 12:40, Andreas Tille  wrote:
> Hi Carnė,
>
> On Fri, Jan 20, 2017 at 05:44:00PM +, Carnė Draug wrote:
>> I have filled a RFP (bug # 852004) for bioperl's Bio-EUtilities
>> package [1].  Unlike Bio-Coordinate, which was split from bioperl and
>> was recently packaged in Debian, Bio-EUtilities development started
>> already after bioperl commenced its splitting.
>>
>> I was wondering if it was possible for the debian-med team to package
>> it.  While I am not a debian maintainer, I am one of the
>> Bio-EUtilities developers, have an interest on seeing it packaged in
>> Debian, and I'm willing to support it upstream.
>
> I have commited some initial packaging to
>
>https://anonscm.debian.org/git/debian-med/libbio-eutilities-perl.git
>
> This build fails due to the failure of several tests - as far as I can
> see due to the attempt to access the internet.  It would help if you
> could provide an option: "Just do all tests than can be done offline"
> since the Debian packaging process needs to run fully offline.
>
> Kind regards
>
>  Andreas.

I have asked on #debian-perl if there was any standard method or
debian preferred method to skip those tests and apparently there is
none.  But there are some suggestions that seem to be common and
acceptable to the Debian.

1. check for an environment variable that defines whether network
tests should be skipped.  Some variables used in Debian are
NO_NETWORK, NOINTERNET, TEST_INTERNET, and NETWORK_TESTING.  See for
example discussion on debian bug #764868 [1]

2. mock EUtilities using Test::LWP::UserAgent.  This is probably the
most involved but probably the technically most correct way.  It has
the problem of not failing if upstream service ever changes (but maybe
if that happens and only the testsuite notices, then this whole module
is not needed).

3. move all tests from t/ to xt/ so that they are only ran at release
time by the package author "since obviously if the author isn't
running their own tests before releasing, you already have a bigger
problem"

Note that the test must not even attempt network access [2] so
skipping the test because a ping to the entrez servers fails is also
not allowed.

I'm CC'ing Chris Fields (also developer on Bio-EUtilities) to discuss
what would Debian and upstream prefer.

Carnë

[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=764868
[2] https://www.debian.org/doc/debian-policy/

Bug#852004: RFP: libbio-eutilities-perl -- bioperl interface to the Entrez Programming Utilities (E-utilities)

2017-01-20 Thread Carnë Draug 
Package: wnpp
Severity: wishlist

* Package name: libbio-eutilities-perl
  Version : 1.75
  Upstream Author : bioperl project 
* URL : https://metacpan.org/release/Bio-EUtilities
* License : Perl
  Programming Lang: Perl
  Description : BioPerl interface to the Entrez Programming Utilities 
(E-utilities)

The Bioperl project is a coordinated effort to collect computational
methods routinely used in bioinformatics into a set of standard
CPAN-style, well-documented, and freely available Perl modules.  This
package provides a programatic interface to NCBI's Entrez Programming
Utilities commonly refered to as E-utilities.  Namely, it provides the
Bio::DB::EUtilities and Bio::Tools::EUtilities perl modules.

Entrez is a federated search engine at the National Center for
Biotechnology Information (NCBI) for a large number of databases
covering a variety of biomedical data, including nucleotide and
protein sequences, gene records, three-dimensional molecular
structures, and the biomedical literature.  E-utilities are a set of
eight server-side programs that provide a stable interface into the
Entrez query and database system at the National Center for
Biotechnology Information (NCBI).

Bug#777383: ITP: python-serpent -- Serpent is a simple serialization python library based on ast.literal_eval

2015-02-07 Thread Carnë Draug 
Package: wnpp
Severity: wishlist
Owner: Carnë Draug carandraug+...@gmail.com

* Package name: python-serpent
  Version : 1.8
  Upstream Author : Irmen de Jong
* URL : https://github.com/irmen/Serpent
* License : MIT
  Programming Lang: Python
  Description : Serpent is a simple serialization python library based on 
ast.literal_eval

Serpent provides ast.literal_eval() compatible object tree serialization.  It 
serializes an
object tree into bytes (utf-8 encoded string) that can be decoded and then 
passed as-is to
ast.literal_eval() to rebuild it as the original object tree.  As such it is 
safe to send
serpent data to other machines over the network for instance (because only 
'safe' literals
are encoded).

Why is this package relevant?  This is a dependency of Pyro4 (see debian bug 
#745437)

How do you pan to maintain it? It is a single source file (serpent.py) so I 
hope it will
not be too much work.  This would also be my first package and seems like a 
good choice for
it.  A mentor would be appreciated.


-- 
To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: https://lists.debian.org/20150207203415.32351.445.reportbug@word

Bug#589818: ensembl-core -- Ensembl core Perl API

2010-08-31 Thread Carnë Draug 
Hi Steffen

the new version came out this month but I haven't managed to package it yet.

This is my first attempt at packaging something and I'm a bit
confused. I was wondering if you could give help me on this one. I've
found a lot of free (as in freedom) software that I need but is not
packaged yet. I don't mind packaging and maintaining them but I don't
know where to start (documentation for new maintainers guide is more
directed for simpler packages).

Hope to hear from you soon. Thanks in advance,
Carnë



--
To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: 
http://lists.debian.org/aanlktik4dwytna5or5s-h-bhrxbvbin5wo5tvqkpr...@mail.gmail.com

Bug#589818: ITP: ensembl-core -- Ensembl core Perl API

2010-07-21 Thread Carnë Draug 
Package: wnpp
Owner: Carnë Draug carandraug...@gmail.com
Severity: wishlist

*** Please type your report below this line ***

* Package name: ensembl-core
  Version : 58
  Upstream Author : Ensembl developers team ensembl-...@ebi.ac.uk
* URL : http://www.ensembl.org/info/docs/api/core/index.html
* License : Other, see
http://www.ensembl.org/info/about/code_licence.html
  Programming Lang: Perl
  Description : Ensembl Core is a Perl API to access the Ensembl Core
databases. It is useful to automate the extraction of particular data, to
customize Ensembl to fulfil a particular purpose, or to store additional data
in Ensembl.



--
To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Archive: 
http://lists.debian.org/aanlktiluwzn-rbxnirqonguz1rh0io5ypcb3uh0no...@mail.gmail.com