[Debian-med-packaging] Bug#984892: unblock: libbio-db-ncbihelper-perl/1.7.6-4

Étienne Mollier etienne.mollier at mailoo.org
Tue Mar 9 19:23:29 GMT 2021 

Package: release.debian.org
Severity: normal
User: release.debian.org at packages.debian.org
Usertags: unblock

Please unblock package libbio-db-ncbihelper-perl

[ Reason ]
Current version of libbio-db-ncbihelper-perl in Testing, in
version 1.7.6-2, is affected by release critical bugs #983239
and #984475.  Due to the autopkgtest now marked "superficial",
I don't expect it will reach Testing on it's own past the hard
freeze date this Friday.

[ Impact ]
Removal of libbio-db-ncbihelper-perl from Testing would trigger
the removal of bioperl, and the entire ecosystem of Med packages
which are based on bioperl.  That represents more than 40 source
packages, some with relatively high popcon by Debian Med
standards.

[ Tests ]
I manually ran the test needing Internet on version 1.7.6-4 in
Sid and Testing, architectures amd64 and arm64 (schroot + qemu),
and modulo the minor failing test which is triggered by events
outside of our control and documented in #983239, they ran fine.
I also ran the build and autopkgtest suite in normal conditions
(superficial) without any issues on Sid and Testing, amd64 and
arm64, just in case.

[ Risks ]
Changes affect diverse test suites to not depend on the network
anymore, so should be more stable, yet superficial.  Also, I
don't see how the Breaks+Replace statement added to the control
file could break the package (but I might be surprised of
course).  Overall I think the risk of upgrading the package in
Testing is rather low.

[ Checklist ]
  [*] all changes are documented in the d/changelog
  [*] I reviewed all changes and I approve them
  [*] attach debdiff against the package in testing

[ Other info ]
The similar libbio-db-embl-perl, which had the same transitive
removal implications, made it's way to Testing fortunately.  But
I'm not too sure of the timing yet for libbio-db-biofetch-perl,
nor it's impact on the bioperl ecosystem.  I might open one
other unblock request for libbio-db-biofetch-perl this week end
if it turns out to be necessary.

unblock libbio-db-ncbihelper-perl/1.7.6-4


Have a nice day,  :)
-- 
Étienne Mollier <etienne.mollier at mailoo.org>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/1, please excuse my verbosity.
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diff -Nru libbio-db-ncbihelper-perl-1.7.6/debian/changelog libbio-db-ncbihelper-perl-1.7.6/debian/changelog
--- libbio-db-ncbihelper-perl-1.7.6/debian/changelog	2020-01-05 07:56:13.000000000 +0100
+++ libbio-db-ncbihelper-perl-1.7.6/debian/changelog	2021-03-04 09:01:01.000000000 +0100
@@ -1,3 +1,24 @@
+libbio-db-ncbihelper-perl (1.7.6-4) unstable; urgency=medium
+
+  * Team upload.
+  * Breaks+Replaces: bioperl (<< 1.7.3)
+    Closes: #984475
+
+ -- Andreas Tille <tille at debian.org>  Thu, 04 Mar 2021 09:01:01 +0100
+
+libbio-db-ncbihelper-perl (1.7.6-3) unstable; urgency=medium
+
+  * Team upload.
+  * Prevent build time tests and autodep8-perl test to fetch resources on the
+    Internet.
+    Closes: #983238
+  * Ensured autopkgtest remained offline, and marked the smoke test as
+    superficial, since all tests within are skipped without Internet access.
+  * Side-tracked maintainer notifications from debian-med at lists.debian.org to
+    debian-med-packaging at lists.alioth.debian.org like the other packages.
+
+ -- Étienne Mollier <etienne.mollier at mailoo.org>  Mon, 22 Feb 2021 22:45:11 +0100
+
 libbio-db-ncbihelper-perl (1.7.6-2) unstable; urgency=medium
 
   * Be more strict about the libbio-asn1-entrezgene-perl dependency
diff -Nru libbio-db-ncbihelper-perl-1.7.6/debian/control libbio-db-ncbihelper-perl-1.7.6/debian/control
--- libbio-db-ncbihelper-perl-1.7.6/debian/control	2020-01-05 07:55:51.000000000 +0100
+++ libbio-db-ncbihelper-perl-1.7.6/debian/control	2021-03-04 09:01:01.000000000 +0100
@@ -1,8 +1,7 @@
 Source: libbio-db-ncbihelper-perl
-Maintainer: Debian Med team <debian-med at lists.debian.org>
-Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Michael R. Crusoe <crusoe at debian.org>
 Section: perl
-Testsuite: autopkgtest-pkg-perl
 Priority: optional
 Build-Depends: debhelper-compat (= 12)
 Build-Depends-Indep: libbio-perl-perl,
@@ -34,6 +33,8 @@
          liburi-perl,
          libwww-perl,
          libxml-twig-perl
+Breaks: bioperl (<< 1.7.3)
+Replaces: bioperl (<< 1.7.3)
 Description: collection of routines useful for queries to NCBI databases
  Provides a single place to setup some common methods for querying NCBI web
  databases. Bio::DB::NCBIHelper just centralizes the methods for constructing
diff -Nru libbio-db-ncbihelper-perl-1.7.6/debian/rules libbio-db-ncbihelper-perl-1.7.6/debian/rules
--- libbio-db-ncbihelper-perl-1.7.6/debian/rules	2020-01-04 12:44:53.000000000 +0100
+++ libbio-db-ncbihelper-perl-1.7.6/debian/rules	2021-03-04 09:01:01.000000000 +0100
@@ -1,10 +1,7 @@
 #!/usr/bin/make -f
 
-ifneq (,$(DEB_MAINTAINER_MODE))
-NETWORK = --network
-else()
-export NO_NETWORK_TESTING
-endif
+# prevent the test suite to fetch resources on the Internet at build time.
+export NO_NETWORK_TESTING=1
 
 %:
 	dh $@
diff -Nru libbio-db-ncbihelper-perl-1.7.6/debian/tests/control libbio-db-ncbihelper-perl-1.7.6/debian/tests/control
--- libbio-db-ncbihelper-perl-1.7.6/debian/tests/control	1970-01-01 01:00:00.000000000 +0100
+++ libbio-db-ncbihelper-perl-1.7.6/debian/tests/control	2021-03-04 09:01:01.000000000 +0100
@@ -0,0 +1,19 @@
+# Pulled from /usr/share/doc/pkg-perl-autopkgtest/examples/default-tests-control
+# This local copy is needed as there is no real point in running the smoke test
+# without Internet connexion, otherwise all tests are skipped, and the test ends
+# up passing while being more than superficial.
+
+Test-Command: /usr/share/pkg-perl-autopkgtest/runner build-deps
+Depends: @, @builddeps@, pkg-perl-autopkgtest
+Restrictions: skippable, superficial
+Features: test-name=autodep8-perl-build-deps
+
+Test-Command: /usr/share/pkg-perl-autopkgtest/runner runtime-deps
+Depends: @, pkg-perl-autopkgtest
+Restrictions: skippable, superficial
+Features: test-name=autodep8-perl
+
+Test-Command: /usr/share/pkg-perl-autopkgtest/runner runtime-deps-and-recommends
+Depends: @, pkg-perl-autopkgtest
+Restrictions: needs-recommends, skippable, superficial
+Features: test-name=autodep8-perl-recommends
diff -Nru libbio-db-ncbihelper-perl-1.7.6/debian/tests/pkg-perl/smoke-env libbio-db-ncbihelper-perl-1.7.6/debian/tests/pkg-perl/smoke-env
--- libbio-db-ncbihelper-perl-1.7.6/debian/tests/pkg-perl/smoke-env	1970-01-01 01:00:00.000000000 +0100
+++ libbio-db-ncbihelper-perl-1.7.6/debian/tests/pkg-perl/smoke-env	2021-03-04 09:01:01.000000000 +0100
@@ -0,0 +1 @@
+NO_NETWORK_TESTING=1
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