Bug#986157: unblock: libchemistry-opensmiles-perl/0.4.3-2
Control: tags -1 confirmed moreinfo
On 2021-03-30 17:57:16, Andrius Merkys wrote:
> Package: release.debian.org
> Severity: normal
> User: release.debian.org@packages.debian.org
> Usertags: unblock
>
> Dear release-team,
>
> I am seeking pre-approval to upload libchemistry-opensmiles-perl/0.4.3-2.
ACK, please remove the moreinfo tag once the version is available in
unstable.
Cheers
>
> [ Reason ]
> libchemistry-opensmiles-perl/0.4.3-1 has a bug which has been fixed
> upstream (also by me). The bug is in code logic detecting aromatic bonds
> in chemical compounds, and as such is not specific to Debian. Fix has
> been released in 0.4.5. libchemistry-opensmiles-perl/0.4.3-2 fixes this
> bug in unstable via patch.
>
> [ Impact ]
> Without the fix, users of libchemistry-opensmiles-perl will observe
> false-negatives in aromatic bond detection.
>
> [ Tests ]
> * Built on clean sid chroot;
> * Upstream regression test for the bug passes.
>
> [ Risks ]
> Changes are minimal and are unlikely to affect other packages
> negatively. Currently libchemistry-opensmiles-perl is a leaf package in
> Debian.
>
> [ Checklist ]
> [*] all changes are documented in the d/changelog
> [*] I reviewed all changes and I approve them
> [*] attach debdiff against the package in testing
>
> unblock libchemistry-opensmiles-perl/0.4.3-2
>
> Best,
> Andrius
>
> diff -Nru libchemistry-opensmiles-perl-0.4.3/debian/changelog libchemistry-opensmiles-perl-0.4.3/debian/changelog
> --- libchemistry-opensmiles-perl-0.4.3/debian/changelog 2021-01-28 05:16:40.000000000 -0500
> +++ libchemistry-opensmiles-perl-0.4.3/debian/changelog 2021-03-30 07:23:23.000000000 -0400
> @@ -1,3 +1,10 @@
> +libchemistry-opensmiles-perl (0.4.3-2) unstable; urgency=medium
> +
> + * Applying upstream commit 6b8267f0bbc87d877bce87bfd28d4538c3f95ee5 as
> + a patch fixing detection of aromatic bonds.
> +
> + -- Andrius Merkys <merkys@debian.org> Tue, 30 Mar 2021 07:23:23 -0400
> +
> libchemistry-opensmiles-perl (0.4.3-1) unstable; urgency=medium
>
> * New upstream version 0.4.3
> diff -Nru libchemistry-opensmiles-perl-0.4.3/debian/patches/6b8267f0bbc87d877bce87bfd28d4538c3f95ee5.patch libchemistry-opensmiles-perl-0.4.3/debian/patches/6b8267f0bbc87d877bce87bfd28d4538c3f95ee5.patch
> --- libchemistry-opensmiles-perl-0.4.3/debian/patches/6b8267f0bbc87d877bce87bfd28d4538c3f95ee5.patch 1969-12-31 19:00:00.000000000 -0500
> +++ libchemistry-opensmiles-perl-0.4.3/debian/patches/6b8267f0bbc87d877bce87bfd28d4538c3f95ee5.patch 2021-03-30 07:19:40.000000000 -0400
> @@ -0,0 +1,36 @@
> +From 6b8267f0bbc87d877bce87bfd28d4538c3f95ee5 Mon Sep 17 00:00:00 2001
> +From: Andrius Merkys <andrius.merkys@gmail.com>
> +Date: Thu, 25 Mar 2021 13:28:22 +0200
> +Subject: [PATCH] Fixing a bug due to incorrectly identified aromatic bond.
> +
> +---
> + lib/Chemistry/OpenSMILES/Parser.yp | 2 +-
> + t/06_write.t | 2 ++
> + 2 files changed, 3 insertions(+), 1 deletion(-)
> +
> +diff --git a/lib/Chemistry/OpenSMILES/Parser.yp b/lib/Chemistry/OpenSMILES/Parser.yp
> +index 8094826..f0e0a13 100644
> +--- a/lib/Chemistry/OpenSMILES/Parser.yp
> ++++ b/lib/Chemistry/OpenSMILES/Parser.yp
> +@@ -60,7 +60,7 @@ chain: atom
> +
> + $_[2]->{graph}->add_edge( $_[1]->{last}, $_[2] );
> +
> +- if( is_aromatic $_[1]->{last} && is_aromatic $_[1]->{last} ) {
> ++ if( is_aromatic $_[1]->{last} && is_aromatic $_[2] ) {
> + $_[2]->{graph}->set_edge_attribute( $_[1]->{last},
> + $_[2],
> + 'bond',
> +diff --git a/t/06_write.t b/t/06_write.t
> +index aee54c5..c0f4656 100644
> +--- a/t/06_write.t
> ++++ b/t/06_write.t
> +@@ -19,6 +19,8 @@ my @cases = (
> + # Chirality information is preserved:
> + [ 'N[C@](Br)(O)C', 'N([C@](Br)(O)(C))' ],
> + [ 'N[C@@](Br)(O)C', 'N([C@@](Br)(O)(C))' ],
> ++ # A regression test for previously incorrectly identified aromatic bond:
> ++ [ 'c1(c(cccc1)F)C(=O)[O-]', 'c:1(:c(:c(:c(:c(:c:1))))(F))(C(=O)([O-]))' ],
> + );
> +
> + plan tests => 2 * scalar @cases;
> diff -Nru libchemistry-opensmiles-perl-0.4.3/debian/patches/series libchemistry-opensmiles-perl-0.4.3/debian/patches/series
> --- libchemistry-opensmiles-perl-0.4.3/debian/patches/series 1969-12-31 19:00:00.000000000 -0500
> +++ libchemistry-opensmiles-perl-0.4.3/debian/patches/series 2021-03-30 07:19:55.000000000 -0400
> @@ -0,0 +1 @@
> +6b8267f0bbc87d877bce87bfd28d4538c3f95ee5.patch
--
Sebastian Ramacher
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