Package: release.debian.org Severity: normal User: release.debian....@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.moll...@mailoo.org> Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/1, please excuse my verbosity.
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 <ti...@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-...@lists.debian.org to
+ debian-med-packag...@lists.alioth.debian.org like the other packages.
+
+ -- Étienne Mollier <etienne.moll...@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-...@lists.debian.org>
-Uploaders: Michael R. Crusoe <michael.cru...@gmail.com>
+Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
+Uploaders: Michael R. Crusoe <cru...@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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