{"app_name":"Debian Janitor","binary_packages":["tophat-recondition"],"branch_url":"git+ssh://git@salsa.debian.org/med-team/tophat-recondition.git","build_distribution":"sid","build_log_highlight_lines":[],"build_log_line_count":1841,"build_log_name":"build.log","campaign":"lintian-fixes","change_set":"e7fa8e39-8d79-4b83-b150-f680cb8cefc4","codebase":"tophat-recondition","codemod_log_name":"codemod.log","command":"DEB_UPDATE_CHANGELOG=auto lintian-brush","current_year":"2026","debdiff":"<p>\nFile lists identical (after any substitutions)\n<p>\nNo differences were encountered in the control files","description":"","is_admin":false,"lintian_result":{"groups":[{"group_id":"tophat-recondition_1.4-4~jan+lint1","input_files":[{"hints":[{"experimental":false,"note":"","pointer":{"item":{"index":"tophat-recondition_1.4-4~jan+lint1.dsc (patched)","name":"debian/changelog"},"line_position":1},"tag":"no-nmu-in-changelog","visibility":"warning"},{"experimental":false,"note":"1.4-4~jan+lint1","pointer":{"item":{"index":"tophat-recondition_1.4-4~jan+lint1.dsc (patched)","name":"debian/changelog"},"line_position":1},"tag":"source-nmu-has-incorrect-version-number","visibility":"warning"}],"path":"tophat-recondition_1.4-4~jan+lint1.dsc"},{"hints":[{"experimental":false,"note":"lintian-fixes != sid","pointer":{"item":{"index":"tophat-recondition_1.4-4~jan+lint1_all.deb (installed)","name":"usr/share/doc/tophat-recondition/changelog.Debian.gz"},"line_position":1},"tag":"changelog-distribution-does-not-match-changes-file","visibility":"warning"},{"experimental":false,"note":"no-manual-page usr/bin/tophat-recondition.py","pointer":{"item":{"index":"tophat-recondition_1.4-4~jan+lint1_all.deb 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(installed)","name":"usr/bin/tophat-recondition.py"},"line_position":0},"tag":"script-with-language-extension","visibility":"warning"}],"path":"tophat-recondition_1.4-4~jan+lint1_all.deb"},{"hints":[],"path":"tophat-recondition_1.4-4~jan+lint1_amd64.buildinfo"},{"hints":[{"experimental":false,"note":"sid lintian-fixes","tag":"distribution-and-changes-mismatch","visibility":"warning"}],"path":"tophat-recondition_1.4-4~jan+lint1_amd64.changes"}],"source_name":"tophat-recondition","source_version":"1.4-4~jan+lint1"}],"lintian_version":"2.135.0"},"logs":{"build":{"description":"build","name":"build.log","url":"/lintian-fixes/c/tophat-recondition/e7fa8e39-8d79-4b83-b150-f680cb8cefc4/logs/build.log"},"codemod":{"description":"codemod","name":"codemod.log","url":"/lintian-fixes/c/tophat-recondition/e7fa8e39-8d79-4b83-b150-f680cb8cefc4/logs/codemod.log"},"worker":{"content":"[2026-05-04T14:59:05Z INFO  janitor_worker] Opening branch at https://salsa.debian.org/med-team/tophat-recondition.git\n[2026-05-04T15:01:23Z INFO  janitor_worker] Cached branch URL http://janitor.debian.net/git/tophat-recondition missing: http://frigg@janitor.debian.net/git/tophat-recondition/\n[2026-05-04T15:01:23Z DEBUG janitor_worker] Workspace path: /srv/worker/output/2/janitor-worker-WsRElX/tophat-recondition\n[2026-05-04T15:01:23Z DEBUG silver_platter::workspace] Creating sprout from git+ssh://git@salsa.debian.org/med-team/tophat-recondition.git\nTotal 73 (delta 0), reused 4 (delta 0), pack-reused 69 (from 1)\nNothing to delete.\n[2026-05-04T15:03:41Z DEBUG silver_platter::workspace] Fetching colocated branches: {}\n[2026-05-04T15:03:41Z INFO  janitor_worker] Workspace ready - starting.\n[2026-05-04T15:03:41Z INFO  janitor_worker::debian] Running [\"lintian-brush\"]\n[2026-05-04T15:03:41Z DEBUG debian_analyzer::detect_gbp_dch] Branch history analysis: changelog_only: 1, other_only: 2, mixed: 6, dch_references: 0, unreleased_references: 4\nfound 28 deltas to reuse\n[2026-05-04T15:03:51Z INFO  ognibuild::debian::fix_build] Using fixers: [PgBuildExtOutOfDateControlFixer, MissingConfigureFixer, MissingAutomakeInputFixer, MissingConfigStatusInputFixer, MissingPerlFileFixer, DebcargoUnacceptablePredicateFixer, DebcargoUnacceptableComparatorFixer, RetryAptFetchFailure, PackageDependencyFixer]\n[2026-05-04T15:03:51Z DEBUG ognibuild::debian::build] Adding dummy changelog entry 1.4-4~jan+lint1 for build\n[2026-05-04T15:03:51Z DEBUG ognibuild::debian::build] Writing build log to /srv/worker/output/2/janitor-worker-WsRElX/build.log\n[2026-05-04T15:03:51Z INFO  ognibuild::debian::build] Building debian packages, running sbuild --chroot-mode=unshare --no-clean-source -A -s -v -d sid.\n[2026-05-04T15:16:55Z INFO  ognibuild::debian::build] Build succeeded.\n[2026-05-04T15:16:55Z INFO  janitor_worker::debian::build] Built [\"/srv/worker/output/2/janitor-worker-WsRElX/tophat-recondition_1.4-4~jan+lint1_amd64.changes\", \"/srv/worker/output/2/janitor-worker-WsRElX/tophat-recondition_1.4-4~jan+lint1_amd64.buildinfo\", \"/srv/worker/output/2/janitor-worker-WsRElX/tophat-recondition_1.4-4~jan+lint1_all.deb\"].\n[2026-05-04T15:16:55Z DEBUG janitor_worker::debian::lintian] Running lintian: cd \"/srv/worker/output/2/janitor-worker-WsRElX\" && \"lintian\" \"--exp-output=format=json\" \"--allow-root\" \"/srv/worker/output/2/janitor-worker-WsRElX/tophat-recondition_1.4-4~jan+lint1_amd64.changes\" \"/srv/worker/output/2/janitor-worker-WsRElX/tophat-recondition_1.4-4~jan+lint1_amd64.buildinfo\" \"/srv/worker/output/2/janitor-worker-WsRElX/tophat-recondition_1.4-4~jan+lint1_all.deb\"\n[2026-05-04T15:16:58Z INFO  janitor_worker] Pushing result branch to http://janitor.debian.net/git/tophat-recondition\n[2026-05-04T15:16:58Z DEBUG janitor_worker::vcs] Symbolic ref creation not yet implemented: refs/heads/lintian-fixes/main -> refs/tags/run/e7fa8e39-8d79-4b83-b150-f680cb8cefc4/main\n[2026-05-04T15:16:58Z DEBUG janitor_worker::vcs] This would create symref refs/heads/lintian-fixes/main pointing to refs/tags/run/e7fa8e39-8d79-4b83-b150-f680cb8cefc4/main\n[2026-05-04T15:16:58Z DEBUG janitor_worker::vcs] Created symref refs/heads/lintian-fixes/main -> refs/tags/run/e7fa8e39-8d79-4b83-b150-f680cb8cefc4/main\n[2026-05-04T15:16:58Z INFO  janitor_worker::vcs] Pushing packaging branch cache to http://janitor.debian.net/git/tophat-recondition\nfound 0 deltas to reuse\n[2026-05-04T15:16:58Z INFO  janitor_worker::vcs] Pushed packaging branch cache to http://janitor.debian.net/git/tophat-recondition\n","description":"worker","name":"worker.log","url":"/lintian-fixes/c/tophat-recondition/e7fa8e39-8d79-4b83-b150-f680cb8cefc4/logs/worker.log"}},"primary_log":"worker","publish_history":[],"queue_position":532,"result":{"applied":[{"certainty":"certain","description":"Update watch file format version to 5.","fixed_lintian_issues":[{"info":"4","package":null,"package_type":"source","tag":"older-debian-watch-file-standard"}],"fixer_name":"debian-watch-file-old-format","overridden_lintian_issues":[],"patch_name":null,"revision_id":"git-v1:b0541b4e8428bb57b5e60b612ee0b2eb2a373330","summary":"Update watch file format version to 5."},{"certainty":"certain","description":"Use GitHub template in watch file instead of explicit Source/Matching-Pattern.","fixed_lintian_issues":[],"fixer_name":"debian-watch-use-templates","overridden_lintian_issues":[],"patch_name":null,"revision_id":"git-v1:4dd03fdcb8c4dff285a31f82b2ec40b1cf6f82a6","summary":"Use GitHub template in watch file instead of explicit Source/Matching-Pattern."},{"certainty":null,"description":"Bump debhelper from old 12 to 13.","fixed_lintian_issues":[{"info":"12","package":null,"package_type":"source","tag":"package-uses-old-debhelper-compat-version"}],"fixer_name":"package-uses-deprecated-debhelper-compat-version","overridden_lintian_issues":[],"patch_name":null,"revision_id":"git-v1:dccbb82e534fe8b5ba6c11d970d1ebc1a322532b","summary":"Bump debhelper from old 12 to 13."},{"certainty":null,"description":"Update renamed lintian tag names in lintian overrides.","fixed_lintian_issues":[{"info":"binary-without-manpage => no-manual-page","package":null,"package_type":"source","tag":"renamed-tag"}],"fixer_name":"renamed-tag","overridden_lintian_issues":[],"patch_name":null,"revision_id":"git-v1:81d6ac414ed33dd2f616404f563fc2fcb76aa286","summary":"Update renamed lintian tag names in lintian overrides."},{"certainty":"certain","description":"Set upstream metadata fields: Bug-Database, Repository, Repository-Browse.","fixed_lintian_issues":[{"info":"[debian/upstream/metadata]","package":null,"package_type":"source","tag":"upstream-metadata-missing-repository"}],"fixer_name":"upstream-metadata-file","overridden_lintian_issues":[],"patch_name":null,"revision_id":"git-v1:ea56024d7bfc15231de079b0aba3f4297b3df46d","summary":"Set upstream metadata fields: Bug-Database, Repository, Repository-Browse."},{"certainty":"certain","description":"Update standards version to 4.7.4, no changes needed.\n\nUpgrade checklist verified:\n 4.5.0 → 4.5.1:\n  * Package does not ship any non-default series files\n 4.5.1 → 4.6.0:\n  * Package does not contain any references to lib64\n 4.6.1 → 4.6.2:\n  * Package does not provide x-window-manager alternative\n 4.6.2 → 4.7.0:\n  * Package does not use dpkg-divert\n 4.7.0 → 4.7.1:\n  * Package does not install to non-/usr paths\n 4.7.3 → 4.7.4:\n  * Package is not in non-free-firmware","fixed_lintian_issues":[{"info":"4.5.0 (released 2020-01-20) (current is 4.7.4.1)","package":null,"package_type":"source","tag":"ancient-standards-version"}],"fixer_name":"out-of-date-standards-version","overridden_lintian_issues":[],"patch_name":null,"revision_id":"git-v1:d65aac7c0de6f6b7c349a6e8365191f94ee598fd","summary":"Update standards version to 4.7.4, no changes needed."}],"changelog_behaviour":{"explanation":"Assuming changelog should be updated","update":true},"failed":{}},"result_code":"success","resume_from":null,"revision":"git-v1:d65aac7c0de6f6b7c349a6e8365191f94ee598fd","run":{"branch_url":"git+ssh://git@salsa.debian.org/med-team/tophat-recondition.git","build_version":null,"change_set":"e7fa8e39-8d79-4b83-b150-f680cb8cefc4","codebase":"tophat-recondition","command":"DEB_UPDATE_CHANGELOG=auto lintian-brush","context":null,"debian_build_distribution":"sid","debian_build_version":null,"description":"","duration_seconds":1074,"failure_stage":null,"failure_transient":null,"finish_time":"2026-05-04T15:16:58.758355Z","id":"e7fa8e39-8d79-4b83-b150-f680cb8cefc4","logfilenames":["build.log","worker.log","codemod.log"],"main_branch_revision":"git-v1:800439e48a8069b754358ab9b4e73db401171459","publish_status":"approved","result":{"applied":[{"certainty":"certain","description":"Update watch file format version to 5.","fixed_lintian_issues":[{"info":"4","package":null,"package_type":"source","tag":"older-debian-watch-file-standard"}],"fixer_name":"debian-watch-file-old-format","overridden_lintian_issues":[],"patch_name":null,"revision_id":"git-v1:b0541b4e8428bb57b5e60b612ee0b2eb2a373330","summary":"Update watch file format version to 5."},{"certainty":"certain","description":"Use GitHub template in watch file instead of explicit Source/Matching-Pattern.","fixed_lintian_issues":[],"fixer_name":"debian-watch-use-templates","overridden_lintian_issues":[],"patch_name":null,"revision_id":"git-v1:4dd03fdcb8c4dff285a31f82b2ec40b1cf6f82a6","summary":"Use GitHub template in watch file instead of explicit Source/Matching-Pattern."},{"certainty":null,"description":"Bump debhelper from old 12 to 13.","fixed_lintian_issues":[{"info":"12","package":null,"package_type":"source","tag":"package-uses-old-debhelper-compat-version"}],"fixer_name":"package-uses-deprecated-debhelper-compat-version","overridden_lintian_issues":[],"patch_name":null,"revision_id":"git-v1:dccbb82e534fe8b5ba6c11d970d1ebc1a322532b","summary":"Bump debhelper from old 12 to 13."},{"certainty":null,"description":"Update renamed lintian tag names in lintian overrides.","fixed_lintian_issues":[{"info":"binary-without-manpage => no-manual-page","package":null,"package_type":"source","tag":"renamed-tag"}],"fixer_name":"renamed-tag","overridden_lintian_issues":[],"patch_name":null,"revision_id":"git-v1:81d6ac414ed33dd2f616404f563fc2fcb76aa286","summary":"Update renamed lintian tag names in lintian overrides."},{"certainty":"certain","description":"Set upstream metadata fields: Bug-Database, Repository, Repository-Browse.","fixed_lintian_issues":[{"info":"[debian/upstream/metadata]","package":null,"package_type":"source","tag":"upstream-metadata-missing-repository"}],"fixer_name":"upstream-metadata-file","overridden_lintian_issues":[],"patch_name":null,"revision_id":"git-v1:ea56024d7bfc15231de079b0aba3f4297b3df46d","summary":"Set upstream metadata fields: Bug-Database, Repository, Repository-Browse."},{"certainty":"certain","description":"Update standards version to 4.7.4, no changes needed.\n\nUpgrade checklist verified:\n 4.5.0 → 4.5.1:\n  * Package does not ship any non-default series files\n 4.5.1 → 4.6.0:\n  * Package does not contain any references to lib64\n 4.6.1 → 4.6.2:\n  * Package does not provide x-window-manager alternative\n 4.6.2 → 4.7.0:\n  * Package does not use dpkg-divert\n 4.7.0 → 4.7.1:\n  * Package does not install to non-/usr paths\n 4.7.3 → 4.7.4:\n  * Package is not in non-free-firmware","fixed_lintian_issues":[{"info":"4.5.0 (released 2020-01-20) (current is 4.7.4.1)","package":null,"package_type":"source","tag":"ancient-standards-version"}],"fixer_name":"out-of-date-standards-version","overridden_lintian_issues":[],"patch_name":null,"revision_id":"git-v1:d65aac7c0de6f6b7c349a6e8365191f94ee598fd","summary":"Update standards version to 4.7.4, no changes needed."}],"changelog_behaviour":{"explanation":"Assuming changelog should be updated","update":true},"failed":{}},"result_branches":[{"absorbed":false,"base_revision":"git-v1:800439e48a8069b754358ab9b4e73db401171459","diff":"diff --git a/debian/changelog b/debian/changelog\nindex fab8afd..afd09e1 100644\n--- a/debian/changelog\n+++ b/debian/changelog\n@@ -1,3 +1,15 @@\n+tophat-recondition (1.4-4) UNRELEASED; urgency=low\n+\n+  * Update watch file format version to 5.\n+  * Use GitHub template in watch file instead of explicit\n+    Source/Matching-Pattern.\n+  * Bump debhelper from old 12 to 13.\n+  * Update renamed lintian tag names in lintian overrides.\n+  * Set upstream metadata fields: Bug-Database, Repository, Repository-Browse.\n+  * Update standards version to 4.7.4, no changes needed.\n+\n+ -- Debian Janitor <janitor@jelmer.uk>  Mon, 04 May 2026 15:03:44 +0000\n+\n tophat-recondition (1.4-3) unstable; urgency=medium\n \n   * Set team. Added Michael as an uploader.\ndiff --git a/debian/control b/debian/control\nindex 0d39870..ce1b0bb 100644\n--- a/debian/control\n+++ b/debian/control\n@@ -4,9 +4,9 @@ Priority: optional\n Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>\n Uploaders: Steffen Moeller <moeller@debian.org>,\n            Michael R. Crusoe <michael.crusoe@gmail.com>\n-Build-Depends: debhelper-compat (= 12)\n+Build-Depends: debhelper-compat (= 13)\n Rules-Requires-Root: no\n-Standards-Version: 4.5.0\n+Standards-Version: 4.7.4\n Homepage: https://github.com/cbrueffer/tophat-recondition\n Vcs-Browser: https://salsa.debian.org/med-team/tophat-recondition\n Vcs-Git: https://salsa.debian.org/med-team/tophat-recondition.git\ndiff --git a/debian/tophat-recondition.lintian-overrides b/debian/tophat-recondition.lintian-overrides\nindex 7ff6489..aa8fc77 100644\n--- a/debian/tophat-recondition.lintian-overrides\n+++ b/debian/tophat-recondition.lintian-overrides\n@@ -1,2 +1,2 @@\n tophat-recondition: script-with-language-extension usr/bin/tophat-recondition.py\n-tophat-recondition: binary-without-manpage usr/bin/tophat-recondition.py\n+tophat-recondition: no-manual-page usr/bin/tophat-recondition.py\ndiff --git a/debian/upstream/metadata b/debian/upstream/metadata\nindex 2ea0901..dccfa10 100644\n--- a/debian/upstream/metadata\n+++ b/debian/upstream/metadata\n@@ -1,3 +1,4 @@\n+Bug-Database: https://github.com/cbrueffer/tophat-recondition/issues\n Reference:\n  Title: A post-processor for TopHat unmapped reads\n  Author: Christian Brueffer and Lao H. Saal\n@@ -14,3 +15,5 @@ Registry:\n    Entry: tophat-recondition\n  - Name: conda:bioconda\n    Entry: tophat-recondition\n+Repository: https://github.com/cbrueffer/tophat-recondition.git\n+Repository-Browse: https://github.com/cbrueffer/tophat-recondition\ndiff --git a/debian/watch b/debian/watch\nindex 0dfe227..36b715d 100644\n--- a/debian/watch\n+++ b/debian/watch\n@@ -1,4 +1,8 @@\n-version=4\n-opts=\"filenamemangle=s%(?:.*?)?v?(\\d[\\d.]*)\\.tar\\.gz%tophat-recondition-$1.tar.gz%\" \\\n-   https://github.com/cbrueffer/tophat-recondition/tags \\\n-   (?:.*?/)?v?(\\d[\\d.]*)\\.tar\\.gz debian uupdate\n+Version: 5\n+\n+Version-Policy: debian\n+Script: uupdate\n+Filenamemangle: s%(?:.*?)?v?(\\d[\\d.]*)\\.tar\\.gz%tophat-recondition-$1.tar.gz%\n+Template: GitHub\n+Owner: cbrueffer\n+Project: tophat-recondition\n","remote_name":"master","revision":"git-v1:d65aac7c0de6f6b7c349a6e8365191f94ee598fd","role":"main"}],"result_code":"success","result_tags":[],"revision":"git-v1:d65aac7c0de6f6b7c349a6e8365191f94ee598fd","start_time":"2026-05-04T14:59:04.559500Z","subpath":"","suite":"lintian-fixes","target_branch_url":null,"vcs_type":"git","worker":"frigg"},"run_id":"e7fa8e39-8d79-4b83-b150-f680cb8cefc4","success_probability":1.0,"suite":"lintian-fixes","total_previous_runs":1,"unchanged_run":{"branch_url":"git+ssh://git@salsa.debian.org/med-team/tophat-recondition.git","build_version":"1.4-3~jan+control1","change_set":"e7fa8e39-8d79-4b83-b150-f680cb8cefc4","codebase":"tophat-recondition","command":"brz up '--revision=git-v1:800439e48a8069b754358ab9b4e73db401171459'","context":null,"debian_build_distribution":"sid","debian_build_version":"1.4-3~jan+control1","description":"No change build","failure_stage":null,"failure_transient":null,"finish_time":"2026-05-05T02:27:37.156623Z","id":"485fc90d-b471-4b96-8ae4-c9861c1fa64a","logfilenames":["worker.log","codemod.log","build.log"],"main_branch_revision":"git-v1:800439e48a8069b754358ab9b4e73db401171459","publish_status":"unknown","result_branches":[],"result_code":"success","result_tags":[],"revision":"git-v1:800439e48a8069b754358ab9b4e73db401171459","start_time":"2026-05-05T02:17:37.932167Z","subpath":"","suite":"control","target_branch_url":null,"vcs_type":"git","worker":"idun"},"utcnow":"2026-05-06T08:31:26.046071177+00:00","vcs_type":"git","vcs_url":"git+ssh://git@salsa.debian.org/med-team/tophat-recondition.git","version":"0.0.0","worker_log_name":"worker.log","worker_name":"frigg"}