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

[Andreas Tille]

On Fri, Jan 27, 2017 at 12:23:22PM +, Carnë Draug wrote:
> 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.

Uploaded to new queue.
 
> > 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.

I'd happily add you as Uploader to the package.  You can feel free to
either maintain it in Debian Med team or move it to pkg-perl at your
preference.  Finally that's another proof that packaging is not that
hard. ;-)

Kind regards
 
Andreas.

-- 
http://fam-tille.de

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

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

[Andreas Tille]

[dropped debian-perl list from CC]

Hi Carnë,

On Thu, Jan 26, 2017 at 06:12:41PM +, Carnë 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.

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 ;-) )

Andreas.

-- 
http://fam-tille.de

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

[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: RFP for bioperl's Bio-EUtilities

[Fields, Christopher J]

On 1/24/17, 2:03 PM, "carandr...@gmail.com on behalf of Carnë Draug" 
 wrote:



>>...
>> 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

Hi Carnë,

Any idea what may be causing this?  I was wondering whether this is an issue 
with a specific XML::SAX parser plugin; I vaguely recall one (I think 
XML::SAX::Expat) causing problems with BLAST XML output b/c it looked for the 
XML DTD locally by default, and if not there it attempted to access the file 
remotely.

chris

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

[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 for bioperl's Bio-EUtilities

[Andreas Tille]

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. :-)

> (Hm, is this the package that was discussed on #debian-perl on IRC
> earlier yesterday? :))

May be - I'm usually not on IRC ...
 
> BTW: I think override_dh_installchangelogs in d/rules is not needed,
> dh_installchangelogs should find Changes by itself.

Thanks, dropped this.

Kind regards

 Andreas.

-- 
http://fam-tille.de

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

[gregor herrmann]

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.

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:

#v+
--- a/debian/rules
+++ b/debian/rules
@@ -1,7 +1,13 @@
 #!/usr/bin/make -f

+TEST_FILES = $(filter-out $(wildcard t/e*.t),$(wildcard t/*.t))
+
 %:
dh $@

 override_dh_installchangelogs:
dh_installchangelogs Changes
+
+override_dh_auto_test:
+   # disable tests which need a network connection
+   dh_auto_test -- TEST_FILES="$(TEST_FILES)"
#v-


Of course an upstream fix, e.g. skipping tests if
$ENV{NETWORK_TESTING} is not set etc., would be nicer.
(Hm, is this the package that was discussed on #debian-perl on IRC
earlier yesterday? :))


BTW: I think override_dh_installchangelogs in d/rules is not needed,
dh_installchangelogs should find Changes by itself.
 

Cheers,
gregor


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

[Fields, Christopher J]

Looks like there are two unrelated errors.  

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?

chris

On 1/23/17, 1:52 PM, "Andreas Tille" <andr...@an3as.eu> wrote:

[CCed debian-perl@l.d.o - discussion is about test failures of new RFPed
 package 
https://anonscm.debian.org/git/debian-med/libbio-eutilities-perl.git]

Hi Christopher,

On Mon, Jan 23, 2017 at 07:25:38PM +, Fields, Christopher J wrote:
> Just ran tests on a non-networked laptop (both latest from Github and the 
1.75 release from CPAN) and they were fine, all passed and the relevant network 
tests are skipped.  Can you be more specific as to the build failure?  

In the download tarball from CPAN the 1.75 release has only a t directory
(no xt).  I've attached the relevant part of the build log.

Hope this helps

  Andreas.
 
> On 1/23/17, 12:46 PM, "Fields, Christopher J" <cjfie...@illinois.edu> 
wrote:
> 
> Actually, when looking at this, the network tests are already in ‘xt’ 
on the repo, and should only tested when making a release:
> 
> https://github.com/bioperl/Bio-EUtilities/tree/master/xt/release
> 
> I’ll pull down the latest CPAN and run it from a non-networked 
computer to see if I can pinpoint what the problem is.
> 
> chris
> 
> On 1/23/17, 9:12 AM, "Fields, Christopher J" <cjfie...@illinois.edu> 
wrote:
> 
> My suggestion is to take the avenue of easiest solution first, 
then most stable solution long-term if needed.  
> 
> The easiest may be to move the network tests to ‘xt’, which as 
Carnė mentioned would be run upon release only.  This should be easy enough w/ 
a Dist::Zilla release.  Longer term a mock setup may be better.
> 
> chris
> 
> On 1/23/17, 9:03 AM, "carandr...@gmail.com on behalf of Carnë 
Draug" <carandr...@gmail.com on behalf of carandraug+...@gmail.com> wrote:
> 
> On 23 January 2017 at 12:40, Andreas Tille <andr...@an3as.eu> 
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 EU

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

[Andreas Tille]

[CCed debian-perl@l.d.o - discussion is about test failures of new RFPed
 package https://anonscm.debian.org/git/debian-med/libbio-eutilities-perl.git]

Hi Christopher,

On Mon, Jan 23, 2017 at 07:25:38PM +, Fields, Christopher J wrote:
> Just ran tests on a non-networked laptop (both latest from Github and the 
> 1.75 release from CPAN) and they were fine, all passed and the relevant 
> network tests are skipped.  Can you be more specific as to the build failure? 
>  

In the download tarball from CPAN the 1.75 release has only a t directory
(no xt).  I've attached the relevant part of the build log.

Hope this helps

  Andreas.
 
> On 1/23/17, 12:46 PM, "Fields, Christopher J" <cjfie...@illinois.edu> wrote:
> 
> Actually, when looking at this, the network tests are already in ‘xt’ on 
> the repo, and should only tested when making a release:
> 
> https://github.com/bioperl/Bio-EUtilities/tree/master/xt/release
> 
> I’ll pull down the latest CPAN and run it from a non-networked computer 
> to see if I can pinpoint what the problem is.
> 
> chris
> 
> On 1/23/17, 9:12 AM, "Fields, Christopher J" <cjfie...@illinois.edu> 
> wrote:
> 
> My suggestion is to take the avenue of easiest solution first, then 
> most stable solution long-term if needed.  
> 
> The easiest may be to move the network tests to ‘xt’, which as Carnė 
> mentioned would be run upon release only.  This should be easy enough w/ a 
> Dist::Zilla release.  Longer term a mock setup may be better.
> 
> chris
> 
> On 1/23/17, 9:03 AM, "carandr...@gmail.com on behalf of Carnë Draug" 
> <carandr...@gmail.com on behalf of carandraug+...@gmail.com> wrote:
> 
> On 23 January 2017 at 12:40, Andreas Tille <andr...@an3as.eu> 
> 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
> prob

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

[Fields, Christopher J]

Andreas,

Just ran tests on a non-networked laptop (both latest from Github and the 1.75 
release from CPAN) and they were fine, all passed and the relevant network 
tests are skipped.  Can you be more specific as to the build failure?  

chris

On 1/23/17, 12:46 PM, "Fields, Christopher J" <cjfie...@illinois.edu> wrote:

Actually, when looking at this, the network tests are already in ‘xt’ on 
the repo, and should only tested when making a release:

https://github.com/bioperl/Bio-EUtilities/tree/master/xt/release

I’ll pull down the latest CPAN and run it from a non-networked computer to 
see if I can pinpoint what the problem is.

chris

On 1/23/17, 9:12 AM, "Fields, Christopher J" <cjfie...@illinois.edu> wrote:

My suggestion is to take the avenue of easiest solution first, then 
most stable solution long-term if needed.  

The easiest may be to move the network tests to ‘xt’, which as Carnė 
mentioned would be run upon release only.  This should be easy enough w/ a 
Dist::Zilla release.  Longer term a mock setup may be better.

chris

On 1/23/17, 9:03 AM, "carandr...@gmail.com on behalf of Carnë Draug" 
<carandr...@gmail.com on behalf of carandraug+...@gmail.com> wrote:

On 23 January 2017 at 12:40, Andreas Tille <andr...@an3as.eu> wrote:
> Hi Carnė,
>
> On Fri, Jan 20, 2017 at 05:44:00PM +0000, 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 fpr bioperl's Bio-EUtilities

[Fields, Christopher J]

Actually, when looking at this, the network tests are already in ‘xt’ on the 
repo, and should only tested when making a release:

https://github.com/bioperl/Bio-EUtilities/tree/master/xt/release

I’ll pull down the latest CPAN and run it from a non-networked computer to see 
if I can pinpoint what the problem is.

chris

On 1/23/17, 9:12 AM, "Fields, Christopher J" <cjfie...@illinois.edu> wrote:

My suggestion is to take the avenue of easiest solution first, then most 
stable solution long-term if needed.  

The easiest may be to move the network tests to ‘xt’, which as Carnė 
mentioned would be run upon release only.  This should be easy enough w/ a 
Dist::Zilla release.  Longer term a mock setup may be better.

chris

On 1/23/17, 9:03 AM, "carandr...@gmail.com on behalf of Carnë Draug" 
<carandr...@gmail.com on behalf of carandraug+...@gmail.com> wrote:

On 23 January 2017 at 12:40, Andreas Tille <andr...@an3as.eu> 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 fpr bioperl's Bio-EUtilities

[Fields, Christopher J]

My suggestion is to take the avenue of easiest solution first, then most stable 
solution long-term if needed.  

The easiest may be to move the network tests to ‘xt’, which as Carnė mentioned 
would be run upon release only.  This should be easy enough w/ a Dist::Zilla 
release.  Longer term a mock setup may be better.

chris

On 1/23/17, 9:03 AM, "carandr...@gmail.com on behalf of Carnë Draug" 
<carandr...@gmail.com on behalf of carandraug+...@gmail.com> wrote:

On 23 January 2017 at 12:40, Andreas Tille <andr...@an3as.eu> 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 fpr bioperl's Bio-EUtilities

[Carnë Draug]

On 23 January 2017 at 12:40, Andreas Tille <andr...@an3as.eu> 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 fpr bioperl's Bio-EUtilities

[Andreas Tille]

Hi Carnë,

On Fri, Jan 20, 2017 at 05:44:00PM +, Carnë 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.

-- 
http://fam-tille.de