[med-svn] [Git][med-team/spades][master] 8 commits: Remove patches not part of d/p/series anymore.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Jun 25 16:52:56 BST 2022
Étienne Mollier pushed to branch master at Debian Med / spades
Commits:
53d089b5 by Étienne Mollier at 2022-06-25T16:45:51+02:00
Remove patches not part of d/p/series anymore.
- - - - -
d2f91d69 by Étienne Mollier at 2022-06-25T17:09:14+02:00
Add fix-privacy-breaches.patch: remove build status badges.
- - - - -
7b8825d1 by Étienne Mollier at 2022-06-25T17:38:57+02:00
Add typos.patch: fix typos caught by lintian.
- - - - -
5be09f9d by Étienne Mollier at 2022-06-25T17:39:43+02:00
d/copyright: reorder to match globbing properly.
- - - - -
6c44f2c1 by Étienne Mollier at 2022-06-25T17:40:16+02:00
d/s/lintian-overrides: unclear why html files are missing source code.
- - - - -
6f90adc2 by Étienne Mollier at 2022-06-25T17:41:04+02:00
update changelog
- - - - -
793477bf by Étienne Mollier at 2022-06-25T17:41:29+02:00
routine-update: Standards-Version: 4.6.1
- - - - -
29ecdabb by Étienne Mollier at 2022-06-25T17:51:27+02:00
routine-update: Ready to upload to unstable
- - - - -
9 changed files:
- debian/changelog
- debian/control
- debian/copyright
- − debian/patches/0111_use_full_config_dirs.patch
- − debian/patches/debug.patch
- + debian/patches/fix-privacy-breaches.patch
- debian/patches/series
- + debian/patches/typos.patch
- debian/source/lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
@@ -1,11 +1,17 @@
-spades (3.15.4+dfsg-3) UNRELEASED; urgency=medium
+spades (3.15.4+dfsg-3) unstable; urgency=medium
* d/t/run-upstreams-tests: make tests a bit more verbose.
* Adjust 0003_accept-system-bwa.patch: import support functions.
(Closes: #1011968)
* Refresh yaml_load.patch.
-
- -- Étienne Mollier <emollier at debian.org> Sat, 25 Jun 2022 16:15:22 +0200
+ * Remove patches not part of d/p/series anymore.
+ * Add fix-privacy-breaches.patch: remove build status badges.
+ * Add typos.patch: fix typos caught by lintian.
+ * d/copyright: reorder to match globbing properly.
+ * d/s/lintian-overrides: unclear why html files are missing source code.
+ * Standards-Version: 4.6.1 (routine-update)
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 25 Jun 2022 17:41:51 +0200
spades (3.15.4+dfsg-2) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -26,7 +26,7 @@ Build-Depends: debhelper-compat (= 13),
bwa,
libbwa-dev,
lynx
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/spades
Vcs-Git: https://salsa.debian.org/med-team/spades.git
Homepage: http://cab.spbu.ru/software/spades/
=====================================
debian/copyright
=====================================
@@ -152,6 +152,12 @@ Files: assembler/ext/include/bamtools/*
Copyright: (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
License: Expat
+Files: assembler/ext/src/samtools/*
+Copyright: (c) 2008-2009 Genome Research Ltd.
+ (c) 2003-2006, 2008-2010 Heng Li
+ (c) 2008 Broad Institute / Massachusetts Institute of Technology
+License: Expat
+
Files: assembler/ext/include/kseq/*
assembler/ext/src/samtools/bcftools/kmin.*
Copyright: (c) 2008-2011 Attractive Chaos <attractor at live.co.uk>
@@ -168,12 +174,6 @@ Copyright: (c) 1992, 1993, 1994 Henry Spencer.
(c) 1992, 1993, 1994 The Regents of the University of California. All rights reserved.
License: BSD-3-clause
-Files: assembler/ext/src/samtools/*
-Copyright: (c) 2008-2009 Genome Research Ltd.
- (c) 2003-2006, 2008-2010 Heng Li
- (c) 2008 Broad Institute / Massachusetts Institute of Technology
-License: Expat
-
Files: assembler/ext/include/cxxopts/*
Copyright: (c) 2014, 2015, 2016 Jarryd Beck
License: Expat
=====================================
debian/patches/0111_use_full_config_dirs.patch deleted
=====================================
@@ -1,47 +0,0 @@
-Description: use full config include path
- This patch makes sure that the config files are not dependent on local
- directory structure.
-Author: Sascha Steinbiss <satta at debian.org>
---- a/assembler/src/spades_pipeline/spades_logic.py
-+++ b/assembler/src/spades_pipeline/spades_logic.py
-@@ -207,6 +207,20 @@ def run_iteration(configs_dir, execution
-
- add_configs(command, dst_configs)
-
-+ for root, dirs, files in os.walk(dst_configs):
-+ replacements = {'#include "': ('#include "' + root + '/')}
-+ for cfg_file in files:
-+ cfg_file = os.path.join(root, cfg_file)
-+ lines = []
-+ with open(cfg_file) as infile:
-+ for line in infile:
-+ for src, target in replacements.iteritems():
-+ line = line.replace(src, target)
-+ lines.append(line)
-+ with open(cfg_file, 'w') as outfile:
-+ for line in lines:
-+ outfile.write(line)
-+
- #print("Calling: " + " ".join(command))
- support.sys_call(command, log)
-
-@@ -254,6 +268,19 @@ def run_scaffold_correction(configs_dir,
- command = [os.path.join(execution_home, "spades-truseq-scfcorrection"), cfg_file_name]
- add_configs(command, dst_configs)
- log.info(str(command))
-+ for root, dirs, files in os.walk(dst_configs):
-+ replacements = {'#include "': ('#include "' + root + '/')}
-+ for cfg_file in files:
-+ cfg_file = os.path.join(root, cfg_file)
-+ lines = []
-+ with open(cfg_file) as infile:
-+ for line in infile:
-+ for src, target in replacements.iteritems():
-+ line = line.replace(src, target)
-+ lines.append(line)
-+ with open(cfg_file, 'w') as outfile:
-+ for line in lines:
-+ outfile.write(line)
- support.sys_call(command, log)
-
-
=====================================
debian/patches/debug.patch deleted
=====================================
@@ -1,38 +0,0 @@
-Description: Some debugging printf's to clarifiy the issue
- Just run
- metaspades.py --test
- or more directly the issue can be debugged in gdb using
- /usr/libexec/spades/spades-hammer ./spades_test/corrected/configs/config.info
- gdb output of last command is:
-
- ...
- ./assembler/ext/src/gqf/gqf.c (591): Debug: last_word = 2, first_word = 774, qf->metadata->bits_per_slot = 8
- ./assembler/ext/src/gqf/gqf.c (596): Debug: last_word = 1
- ./assembler/ext/src/gqf/gqf.c (591): Debug: last_word = 1, first_word = 774, qf->metadata->bits_per_slot = 8
- ./assembler/ext/src/gqf/gqf.c (596): Debug: last_word = 0
- ./assembler/ext/src/gqf/gqf.c (591): Debug: last_word = 0, first_word = 774, qf->metadata->bits_per_slot = 8
-
- Thread 4 "spades-hammer" received signal SIGSEGV, Segmentation fault.
- [Switching to Thread 0x7ffff6a1e700 (LWP 1670144)]
- 0x00005555555e91d9 in shift_into_b (amount=8, bend=64, bstart=0, b=0, a=<error reading variable: Cannot access memory at address 0x20000636610afff8>)
- at ./assembler/ext/src/gqf/gqf.c:541
- warning: Source file is more recent than executable.
- 541 const uint64_t a_component = bstart == 0 ? (a >> (64 - amount)) : 0;
-
---- a/assembler/ext/src/gqf/gqf.c
-+++ b/assembler/ext/src/gqf/gqf.c
-@@ -586,11 +586,14 @@ static inline void shift_remainders(QF *
-
- assert(start_index <= empty_index && empty_index < qf->metadata->xnslots);
- assert(first_word <= last_word);
-+ printf("%s (%i): Debug: qf->metadata->bits_per_slot = %i\n", __FILE__, __LINE__, qf->metadata->bits_per_slot);
- while (last_word != first_word) {
-+ printf("%s (%i): Debug: last_word = %i, first_word = %i, qf->metadata->bits_per_slot = %i\n", __FILE__, __LINE__, last_word, first_word, qf->metadata->bits_per_slot);
- *REMAINDER_WORD(qf, last_word) = shift_into_b(*REMAINDER_WORD(qf, last_word-1),
- *REMAINDER_WORD(qf, last_word),
- 0, bend, qf->metadata->bits_per_slot);
- last_word--;
-+ printf("%s (%i): Debug: last_word = %i\n", __FILE__, __LINE__, last_word);
- bend = 64;
- }
- *REMAINDER_WORD(qf, last_word) = shift_into_b(0, *REMAINDER_WORD(qf, last_word),
=====================================
debian/patches/fix-privacy-breaches.patch
=====================================
@@ -0,0 +1,20 @@
+Description: fix privacy breaches identified by lintian.
+ These breaches are caused by various badges, they may be safely remove.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: not-needed
+Last-Update: 2022-06-25
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- spades.orig/assembler/manual.html
++++ spades/assembler/manual.html
+@@ -1,9 +1,4 @@
+-<html> <head> <title>SPAdes 3.15.4 Manual</title> <style type="text/css"> .highlight pre { background-color: #f0f2f4; border-radius: 2px; font-size: 100%; line-height: 1.45; overflow: auto; padding: 16px; } </style> </head> <body><p dir="auto"><a href="http://chihua.cab.spbu.ru:3000/buildConfiguration/SPAdesBasicTests_RunAll?mode=builds" rel="nofollow"><img src="https://camo.githubusercontent.com/21b928ad15b5735360cb555da4951c8dee2ef5633fd61c3fce22bb157f9dc1c5/687474703a2f2f6368696875612e6361622e737062752e72753a333030302f6170702f726573742f6275696c64732f6275696c64547970653a2869643a535041646573426173696354657374735f52756e416c6c292f73746174757349636f6e" alt="TeamCity Simple Build Status" data-canonical-src="http://chihua.cab.spbu.ru:3000/app/rest/builds/buildType:(id:SPAdesBasicTests_RunAll)/statusIcon" style="max-width: 100%;"></a><br>
+-<a href="https://www.gnu.org/licenses/old-licenses/gpl-2.0" rel="nofollow"><img src="https://camo.githubusercontent.com/c76156a44047d8a6b64fc1fa16118996c422cff2959c1ae82127260b29e990ef/68747470733a2f2f696d672e736869656c64732e696f2f62616467652f6c6963656e63652d47504c76322d626c7565" alt="License" data-canonical-src="https://img.shields.io/badge/licence-GPLv2-blue" style="max-width: 100%;"></a><br>
+-<a href="https://github.com/ablab/spades/releases/"><img src="https://camo.githubusercontent.com/b67a7145a28ab5560f54b811c18353c4771fa5ae62a344f4d5e53a4c0a9da5b4/68747470733a2f2f696d672e736869656c64732e696f2f6769746875622f762f72656c656173652f61626c61622f737061646573" alt="GitHub release (latest by date)" data-canonical-src="https://img.shields.io/github/v/release/ablab/spades" style="max-width: 100%;"></a><br>
+-<a href="https://github.com/ablab/spades/releases"><img src="https://camo.githubusercontent.com/a8ba4fbdefabcc61b7a4d41a40fb19c92e96d49717bd24414252a4f460a34f09/68747470733a2f2f696d672e736869656c64732e696f2f6769746875622f646f776e6c6f6164732f61626c61622f7370616465732f746f74616c2e7376673f7374796c653d736f6369616c266c6f676f3d676974687562266c6162656c3d446f776e6c6f6164" alt="GitHub Downloads" data-canonical-src="https://img.shields.io/github/downloads/ablab/spades/total.svg?style=social&logo=github&label=Download" style="max-width: 100%;"></a><br>
+-<a href="https://anaconda.org/bioconda/spades" rel="nofollow"><img src="https://camo.githubusercontent.com/24a3286de783bcb188f9e010b910a26db4026ecf4b05f184fb3f71f4892f6c77/68747470733a2f2f616e61636f6e64612e6f72672f62696f636f6e64612f7370616465732f6261646765732f646f776e6c6f6164732e737667" alt="BioConda Downloads" data-canonical-src="https://anaconda.org/bioconda/spades/badges/downloads.svg" style="max-width: 100%;"></a><br>
+-<a href="code_of_conduct.md"><img src="https://camo.githubusercontent.com/9a5e1f5558bc77986d831a81a6f80819da5a94c13d3aca339a0993119f535a06/68747470733a2f2f696d672e736869656c64732e696f2f62616467652f436f6e7472696275746f72253230436f76656e616e742d322e302d3462616161612e737667" alt="Contributor Covenant" data-canonical-src="https://img.shields.io/badge/Contributor%20Covenant-2.0-4baaaa.svg" style="max-width: 100%;"></a></p>
++<html> <head> <title>SPAdes 3.15.4 Manual</title> <style type="text/css"> .highlight pre { background-color: #f0f2f4; border-radius: 2px; font-size: 100%; line-height: 1.45; overflow: auto; padding: 16px; } </style> </head> <body>
+ <p dir="auto"><strong>SPAdes 3.15.4 Manual</strong></p>
+ <ol dir="auto">
+ <li><a href="#sec1">About SPAdes</a> <br>
=====================================
debian/patches/series
=====================================
@@ -18,3 +18,5 @@ debian_bwa_zlib.patch
workdir_for_test.patch
disable_local_convertutf.patch
fix-sigill-on-non-popcnt-cpus.patch
+fix-privacy-breaches.patch
+typos.patch
=====================================
debian/patches/typos.patch
=====================================
@@ -0,0 +1,17 @@
+Description: fix typo caught by lintian.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2022-06-25
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- spades.orig/assembler/src/common/stages/ss_edge_split.hpp
++++ spades/assembler/src/common/stages/ss_edge_split.hpp
+@@ -14,7 +14,7 @@
+ class SSEdgeSplit: public spades::AssemblyStage {
+
+ public:
+- SSEdgeSplit() : AssemblyStage("Strand-specific Edge Spliting", "ss_edge_splitting") {}
++ SSEdgeSplit() : AssemblyStage("Strand-specific Edge Splitting", "ss_edge_splitting") {}
+
+ void run(GraphPack& gp, const char *) override;
+ };
=====================================
debian/source/lintian-overrides
=====================================
@@ -1,2 +1,4 @@
# Upstream does not provide signed tarballs
spades source: debian-watch-does-not-check-gpg-signature
+# For some reason these html files are considered like binaries
+spades source: source-is-missing [assembler/*.html]
View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/88edc5574662f6d3b8b46b6087817b251175dee6...29ecdabb8a879e5b8a06b286f3ceff0ec82a56b0
--
View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/88edc5574662f6d3b8b46b6087817b251175dee6...29ecdabb8a879e5b8a06b286f3ceff0ec82a56b0
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