Your message dated Wed, 12 Apr 2023 06:49:21 +0000
with message-id <[email protected]>
and subject line Bug#1004053: fixed in kallisto 0.48.0+dfsg-4
has caused the Debian Bug report #1004053,
regarding kallisto: reproducible-builds: timestamps and build path embedded in
test suite metadata
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1004053: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1004053
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: kallisto
Severity: normal
Tags: patch
User: [email protected]
Usertags: buildpath timestamps
X-Debbugs-Cc: [email protected]
Various files produced related to test suites embed timestamp and build
paths into the files, breaking reproducible builds:
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/diffoscope-results/kallisto.html
It looks like version 0.48.0+dfsg-1 introduced these new files, with the
introduction of the snakemake tests.
The attached patch fixes this by removing the test suite log files and
other test suite metadata in a dh_install override from debian/rules.
With this patch applied, kallisto should build reproducibly on
tests.reproducible-builds.org!
Thanks for maintaining kallisto!
live well,
vagrant
From 5c5e9ba026cb5acb27cca8ede0ddc41015b879c4 Mon Sep 17 00:00:00 2001
From: Vagrant Cascadian <[email protected]>
Date: Wed, 19 Jan 2022 22:58:14 +0000
Subject: [PATCH] debian/rules: Remove various test suite log files and
metadata.
Various differences including timestamps, timing information, and
build paths are embedded in these files, which make it nearly
impossible to build the package reproducibly.
https://tests.reproducible-builds.org/debian/issues/unstable/test_suite_logs_issue.html
---
debian/rules | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/debian/rules b/debian/rules
index 23ee80e..3d9a422 100755
--- a/debian/rules
+++ b/debian/rules
@@ -17,3 +17,10 @@ override_dh_auto_configure:
override_dh_auto_test:
dh_auto_test
cd test && PATH=$$(find ../obj-* -name src):$(PATH) HOME=$$(mktemp --directory) snakemake --cores 1
+
+override_dh_install:
+ dh_install
+ # Remove test suite logs and other metadata about the test suite
+ rm -rvf debian/kallisto-examples/usr/share/doc/kallisto/test/.snakemake
+ rm -vf debian/kallisto-examples/usr/share/doc/kallisto/test/bus_out/run_info.json
+ rm -vf debian/kallisto-examples/usr/share/doc/kallisto/test/quant_out/run_info.json
--
2.34.1
signature.asc
Description: PGP signature
--- End Message ---
--- Begin Message ---
Source: kallisto
Source-Version: 0.48.0+dfsg-4
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
kallisto, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated kallisto package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 12 Apr 2023 07:44:19 +0200
Source: kallisto
Architecture: source
Version: 0.48.0+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1004053
Changes:
kallisto (0.48.0+dfsg-4) unstable; urgency=medium
.
[ Vagrant Cascadian ]
* Remove quant_out/run_info.json to enable reproducible-builds
Closes: #1004053
Checksums-Sha1:
536346bc06d6f8faa43e2eb71cf2b6e6a4fc0e4a 2287 kallisto_0.48.0+dfsg-4.dsc
5f317432603d010f34dd9935d6cc43f18e4a4394 7116
kallisto_0.48.0+dfsg-4.debian.tar.xz
872bf780c01c2a112e0d51d2a4a3c43838822321 12121
kallisto_0.48.0+dfsg-4_amd64.buildinfo
Checksums-Sha256:
50e5b11ec43a502627fa1923db864ed909300622ecfad24634c0f2ef71622006 2287
kallisto_0.48.0+dfsg-4.dsc
f0fa8ca0d2bb8ce6210e2c7725547397adc0e8520e3703889289524308e9b298 7116
kallisto_0.48.0+dfsg-4.debian.tar.xz
71f8b59b7da51e2e0c7975094f56c567a6f8528514d32f19e9017b0cf1a67685 12121
kallisto_0.48.0+dfsg-4_amd64.buildinfo
Files:
3000408d585ba2f6a36fe38e19a9032c 2287 science optional
kallisto_0.48.0+dfsg-4.dsc
8e5675599154f7503ab32dff51b39063 7116 science optional
kallisto_0.48.0+dfsg-4.debian.tar.xz
d99f7c9259eec9e5f0078da140b6d4f6 12121 science optional
kallisto_0.48.0+dfsg-4_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----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=ZtOU
-----END PGP SIGNATURE-----
--- End Message ---
