[med-svn] [Git][med-team/sra-sdk][master] 11 commits: Start work on sra-sdk 3.2.1+dfsg-6.
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Fri Feb 27 22:51:59 GMT 2026
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
375878ca by Aaron M. Ucko at 2026-02-27T17:21:35-05:00
Start work on sra-sdk 3.2.1+dfsg-6.
- - - - -
1948a278 by Aaron M. Ucko at 2026-02-27T17:42:24-05:00
Obtain re2's dependencies from pkgconf or pkg-config (#1126172).
* debian/control: Build-depend on pkgconf (or pkg-config).
* debian/patches/support_libre2-11.patch: Obtain re2's dependencies from
pkgconf or pkg-config rather than hardcoding absl_string_view.
(Closes: #1126172, modulo the need for a rebuilt re2.)
- - - - -
6cfbdeab by Aaron M. Ucko at 2026-02-27T17:43:05-05:00
Add support_glibc_2.43.patch against agrep-main.c (#1128753).
Comment out gratuitous redefinition of index as an alias for strchr,
which interacted poorly with C23 const-preserving generics.
- - - - -
3bcb876d by Aaron M. Ucko at 2026-02-27T17:43:35-05:00
Standards-Version: 4.7.3 (routine-update)
- - - - -
fed03b7f by Aaron M. Ucko at 2026-02-27T17:44:54-05:00
Update watch file format version to 5.
Changes-By: lintian-brush
Fixes: lintian: older-debian-watch-file-standard
See-also: https://lintian.debian.org/tags/older-debian-watch-file-standard.html
- - - - -
043b9e56 by Aaron M. Ucko at 2026-02-27T17:45:00-05:00
Add dversionmangle for repack versioning in debian/watch.
Changes-By: lintian-brush
Fixes: lintian: debian-watch-not-mangling-version
See-also: https://lintian.debian.org/tags/debian-watch-not-mangling-version.html
- - - - -
132763e9 by Aaron M. Ucko at 2026-02-27T17:45:00-05:00
Use GitHub template in watch file instead of explicit Source/Matching-Pattern.
Changes-By: lintian-brush
- - - - -
18ffa5eb by Aaron M. Ucko at 2026-02-27T17:45:00-05:00
Reorder Files paragraphs in debian/copyright by directory depth.
Changes-By: lintian-brush
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html
- - - - -
d7bdcafe by Aaron M. Ucko at 2026-02-27T17:45:00-05:00
Remove duplicate values for fields Entry, Entry, Entry, Name, Name in debian/upstream/metadata.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-yaml-invalid
See-also: https://lintian.debian.org/tags/upstream-metadata-yaml-invalid.html
- - - - -
5ef13b37 by Aaron M. Ucko at 2026-02-27T17:45:00-05:00
debputy lint --auto-fix (routine-update)
- - - - -
ad18e223 by Aaron M. Ucko at 2026-02-27T17:45:36-05:00
Finalize sra-sdk 3.2.1+dfsg-6 for unstable.
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/series
- + debian/patches/support_glibc_2.43.patch
- debian/patches/support_libre2-11.patch
- debian/upstream/metadata
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,24 @@
+sra-sdk (3.2.1+dfsg-6) unstable; urgency=medium
+
+ * debian/control: Build-depend on pkgconf.
+ * debian/patches/support_glibc_2.43.patch (new): Comment out
+ test/search/agrep-main.c's gratuitous redefinition of index as an alias
+ for strchr, which interacted poorly with C23 const-preserving generics.
+ (Closes: #1128753.)
+ * debian/patches/support_libre2-11.patch: Obtain re2's dependencies from
+ pkgconf rather than hardcoding absl_string_view. (Closes: #1126172,
+ modulo the need for a rebuilt re2.)
+ * Update watch file format version to 5.
+ * Add dversionmangle for repack versioning in debian/watch.
+ * Use GitHub template in watch file instead of explicit
+ Source/Matching-Pattern.
+ * Reorder Files paragraphs in debian/copyright by directory depth.
+ * Remove duplicate values for fields Entry, Entry, Entry, Name, Name in
+ debian/upstream/metadata.
+ * debputy lint --auto-fix (routine-update)
+
+ -- Aaron M. Ucko <ucko at debian.org> Fri, 27 Feb 2026 17:45:36 -0500
+
sra-sdk (3.2.1+dfsg-5) unstable; urgency=medium
* debian/patches/bypass-libxml2-ATTRIBUTE_UNUSED.patch (new): Fix builds
=====================================
debian/control
=====================================
@@ -20,13 +20,14 @@ Build-Depends: debhelper-compat (= 13),
liblzma-dev,
libsam-extract-dev,
maven-repo-helper,
+ pkgconf,
python3-all,
python3-setuptools,
python3-vdb,
default-jdk,
flex,
bison
-Standards-Version: 4.7.2
+Standards-Version: 4.7.3
Vcs-Browser: https://salsa.debian.org/med-team/sra-sdk
Vcs-Git: https://salsa.debian.org/med-team/sra-sdk.git
Homepage: https://github.com/ncbi/sra-tools/
=====================================
debian/copyright
=====================================
@@ -29,47 +29,6 @@ License: public-domain
.
Please cite the author in any work or product based on this material.
-Files: debian/tests/test-data/test-data.tar.gz
-Copyright: 1996-2018 NCBI
-License: unrestricted
- Databases of molecular data on the NCBI Web site include such examples as
- nucleotide sequences (GenBank), protein sequences, macromolecular
- structures, molecular variation, gene expression, and mapping data. They
- are designed to provide and encourage access within the scientific
- community to sources of current and comprehensive information. Therefore,
- NCBI itself places no restrictions on the use or distribution of the data
- contained therein. Nor do we accept data when the submitter has requested
- restrictions on reuse or redistribution.
-Comment:
- The test data files contained in the archive are a data set prepared from
- original SRAs with accession numbers SRR6650398, SRR2042184 and SRR7032226.
-
-Files: ngs/ngs-sdk/language/java/jni*.h ngs/ncbi/ngs-jni/jni*.h
-Copyright: 1996, Netscape Communications Corporation
- 2006, Oracle and/or its affiliates
-License: GPL-2
- This code is free software; you can redistribute it and/or modify it
- under the terms of the GNU General Public License version 2 only, as
- published by the Free Software Foundation. Oracle designates this
- particular file as subject to the "Classpath" exception as provided
- by Oracle in the LICENSE file that accompanied this code.
- .
- This code is distributed in the hope that it will be useful, but WITHOUT
- ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
- version 2 for more details (a copy is included in the LICENSE file that
- accompanied this code).
- .
- You should have received a copy of the GNU General Public License
- along with this package; if not, see https://www.gnu.org/licenses/.
- .
- Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
- or visit www.oracle.com if you need additional information or have any
- questions.
- .
- We used part of Netscape's Java Runtime Interface (JRI) as the starting
- point of our design and implementation.
-
Files: tools/loaders/fastq-loader/fastq-tokens.h
tools/loaders/fastq-loader/zz_fastq-grammar.?
Copyright: 1984, 1989-1990, 2000-2015, 2018-2020 Free Software Foundation, Inc.
@@ -122,14 +81,6 @@ License: Apache-2
On Debian systems you can find a copy of the Apache License, version
2.0, at /usr/share/common-licenses/Apache-2.0.
-Files: tools/loaders/sharq/hash/*
-Copyright: 2017-2020 Mike Tzou (Chocobo1)
-License: GPL-3+
-
-Files: tools/loaders/sharq/hash/gsl/*
-Copyright: 2015 Microsoft Corporation
-License: Expat
-
Files: tools/loaders/sharq/json.hpp
Copyright: 2008-2009 Bjoern Hoehrmann <bjoern at hoehrmann.de>
2009 Florian Loitsch
@@ -140,6 +91,55 @@ Files: libs/inc/spdlog/*
Copyright: 2015-2021, Gabi Melman & spdlog contributors.
License: Expat
+Files: ngs/ngs-sdk/language/java/jni*.h ngs/ncbi/ngs-jni/jni*.h
+Copyright: 1996, Netscape Communications Corporation
+ 2006, Oracle and/or its affiliates
+License: GPL-2
+ This code is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License version 2 only, as
+ published by the Free Software Foundation. Oracle designates this
+ particular file as subject to the "Classpath" exception as provided
+ by Oracle in the LICENSE file that accompanied this code.
+ .
+ This code is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+ version 2 for more details (a copy is included in the LICENSE file that
+ accompanied this code).
+ .
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, see https://www.gnu.org/licenses/.
+ .
+ Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
+ or visit www.oracle.com if you need additional information or have any
+ questions.
+ .
+ We used part of Netscape's Java Runtime Interface (JRI) as the starting
+ point of our design and implementation.
+
+Files: tools/loaders/sharq/hash/*
+Copyright: 2017-2020 Mike Tzou (Chocobo1)
+License: GPL-3+
+
+Files: tools/loaders/sharq/hash/gsl/*
+Copyright: 2015 Microsoft Corporation
+License: Expat
+
+Files: debian/tests/test-data/test-data.tar.gz
+Copyright: 1996-2018 NCBI
+License: unrestricted
+ Databases of molecular data on the NCBI Web site include such examples as
+ nucleotide sequences (GenBank), protein sequences, macromolecular
+ structures, molecular variation, gene expression, and mapping data. They
+ are designed to provide and encourage access within the scientific
+ community to sources of current and comprehensive information. Therefore,
+ NCBI itself places no restrictions on the use or distribution of the data
+ contained therein. Nor do we accept data when the submitter has requested
+ restrictions on reuse or redistribution.
+Comment:
+ The test data files contained in the archive are a data set prepared from
+ original SRAs with accession numbers SRR6650398, SRR2042184 and SRR7032226.
+
License: Expat
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
=====================================
debian/patches/series
=====================================
@@ -45,3 +45,4 @@ setuptools.patch
fix_bm_for_gcc15.patch
include_cstdint_for_gcc15.patch
bypass-libxml2-ATTRIBUTE_UNUSED.patch
+support_glibc_2.43.patch
=====================================
debian/patches/support_glibc_2.43.patch
=====================================
@@ -0,0 +1,13 @@
+Index: b/test/search/agrep-main.c
+===================================================================
+--- a/test/search/agrep-main.c
++++ b/test/search/agrep-main.c
+@@ -23,7 +23,7 @@
+ * ===========================================================================
+ *
+ */
+-#define index strchr
++/*#define index strchr*/
+ #include <search/extern.h>
+ #include <sysalloc.h>
+ #include "../../libs/search/search-priv.h"
=====================================
debian/patches/support_libre2-11.patch
=====================================
@@ -1,3 +1,5 @@
+Index: b/tools/loaders/sharq/regexpr.hpp
+===================================================================
--- a/tools/loaders/sharq/regexpr.hpp
+++ b/tools/loaders/sharq/regexpr.hpp
@@ -11,6 +11,7 @@
@@ -17,6 +19,8 @@
return re2::RE2::PartialMatchN(input, *re, args.empty() ? nullptr : &args[0], (int)args.size());
}
+Index: b/test/loaders/sharq/test-regexpr.cpp
+===================================================================
--- a/test/loaders/sharq/test-regexpr.cpp
+++ b/test/loaders/sharq/test-regexpr.cpp
@@ -60,17 +60,17 @@ TEST_CASE(YesMatch)
@@ -48,6 +52,8 @@
}
int main (int argc, char *argv [])
+Index: b/tools/loaders/sharq/fastq_defline_matcher.hpp
+===================================================================
--- a/tools/loaders/sharq/fastq_defline_matcher.hpp
+++ b/tools/loaders/sharq/fastq_defline_matcher.hpp
@@ -9,6 +9,7 @@
@@ -441,6 +447,8 @@
spot_group.remove_prefix(1);
read.SetSpotGroup(spot_group);
auto& read_num = re.GetMatch()[2];
+Index: b/tools/loaders/sharq/fastq_read.hpp
+===================================================================
--- a/tools/loaders/sharq/fastq_read.hpp
+++ b/tools/loaders/sharq/fastq_read.hpp
@@ -60,23 +60,23 @@ public:
@@ -481,6 +489,8 @@
}
+Index: b/tools/loaders/sharq/fastq_defline_parser.hpp
+===================================================================
--- a/tools/loaders/sharq/fastq_defline_parser.hpp
+++ b/tools/loaders/sharq/fastq_defline_parser.hpp
@@ -57,7 +57,7 @@ public:
@@ -528,6 +538,8 @@
mDefLineMatchers[mIndexLastSuccessfulMatch]->GetMatch(read);
return;
}
+Index: b/tools/loaders/sharq/fastq_parser.hpp
+===================================================================
--- a/tools/loaders/sharq/fastq_parser.hpp
+++ b/tools/loaders/sharq/fastq_parser.hpp
@@ -847,7 +847,7 @@ bool fastq_reader::parse_read(CFastqRead
@@ -539,6 +551,8 @@
m_buffered_defline = m_line;
break;
}
+Index: b/tools/loaders/sharq/CMakeLists.txt
+===================================================================
--- a/tools/loaders/sharq/CMakeLists.txt
+++ b/tools/loaders/sharq/CMakeLists.txt
@@ -92,7 +92,7 @@ if( SINGLE_CONFIG )
@@ -546,10 +560,12 @@
# -DCMAKE_OSX_DEPLOYMENT_TARGET=${CMAKE_OSX_DEPLOYMENT_TARGET}
# )
- set(RE2_STATIC_LIBRARIES -lre2 )
-+ set(RE2_STATIC_LIBRARIES -lre2 -labsl_string_view)
++ #set(RE2_STATIC_LIBRARIES -lre2 )
add_custom_target(
sharq.py
+Index: b/test/loaders/sharq/CMakeLists.txt
+===================================================================
--- a/test/loaders/sharq/CMakeLists.txt
+++ b/test/loaders/sharq/CMakeLists.txt
@@ -50,7 +50,7 @@ message(RE2_FOUND=${RE2_FOUND})
@@ -557,7 +573,22 @@
set(LOCAL_INCDIR ${LOCAL_BUILD_DIR}/include)
set(LOCAL_LIBDIR ${LOCAL_BUILD_DIR}/lib)
- set(RE2_STATIC_LIBRARIES -lre2 )
-+ set(RE2_STATIC_LIBRARIES -lre2 -labsl_string_view)
++ #set(RE2_STATIC_LIBRARIES -lre2 )
if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU" OR CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
set(CXX_FILESYSTEM_LIBRARIES "stdc++fs")
+Index: b/build/env.cmake
+===================================================================
+--- a/build/env.cmake
++++ b/build/env.cmake
+@@ -263,6 +263,10 @@ if ( PYTHON_PATH )
+ endif()
+ find_package( Python3 COMPONENTS Interpreter )
+
++find_package( PkgConfig )
++pkg_check_modules( RE2 re2 )
++set( RE2_STATIC_LIBRARIES ${RE2_LIBRARIES} )
++
+ # ===========================================================================
+ # testing
+
=====================================
debian/upstream/metadata
=====================================
@@ -1,34 +1,29 @@
Bug-Database: https://github.com/ncbi/sra-tools/issues
Bug-Submit: https://github.com/ncbi/sra-tools/issues/new
Reference:
- Author: >
- Rasko Leinonen and Ruth Akhtar and Ewan Birney and James Bonfield and
- Lawrence Bower and Matt Corbett and Ying Cheng and Fehmi Demiralp and
- Nadeem Faruque and Neil Goodgame and Richard Gibson and Gemma Hoad
- and Christopher Hunter and Mikyung Jang and Steven Leonard and Quan
- Lin and Rodrigo Lopez and Michael Maguire and Hamish McWilliam and
- Sheila Plaister and Rajesh Radhakrishnan and Siamak Sobhany and Guy
- Slater and Petra Ten Hoopen and Franck Valentin and Robert Vaughan
- and Vadim Zalunin and Daniel Zerbino and Guy Cochrane
- Title: Improvements to services at the European Nucleotide Archive
- Journal: Nucleic Acids Research
- Year: 2010
- Volume: 38
- Number: Database issue
- Pages: D39-45
- DOI: 10.1093/nar/gkp998
- PMID: 19906712
- URL: http://nar.oxfordjournals.org/content/38/suppl_1/D39
- eprint: >
- http://nar.oxfordjournals.org/content/38/suppl_1/D39.full.pdf+html
+ Author: >
+ Rasko Leinonen and Ruth Akhtar and Ewan Birney and James Bonfield and:
+ Lawrence Bower and Matt Corbett and Ying Cheng and Fehmi Demiralp and:
+ Nadeem Faruque and Neil Goodgame and Richard Gibson and Gemma Hoad:
+ and Christopher Hunter and Mikyung Jang and Steven Leonard and Quan:
+ Lin and Rodrigo Lopez and Michael Maguire and Hamish McWilliam and:
+ Sheila Plaister and Rajesh Radhakrishnan and Siamak Sobhany and Guy:
+ Slater and Petra Ten Hoopen and Franck Valentin and Robert Vaughan:
+ and Vadim Zalunin and Daniel Zerbino and Guy Cochrane:
+ Title: Improvements to services at the European Nucleotide Archive
+ Journal: Nucleic Acids Research
+ Year: 2010
+ Volume: 38
+ Number: Database issue
+ Pages: D39-45
+ DOI: 10.1093/nar/gkp998
+ PMID: 19906712
+ URL: http://nar.oxfordjournals.org/content/38/suppl_1/D39
+ eprint: >
+ http://nar.oxfordjournals.org/content/38/suppl_1/D39.full.pdf+html: null
Registry:
- - Name: bio.tools
- Entry: sra-tools
- - Name: SciCrunch
- Entry: NA
- - Name: OMICtools
- Entry: OMICS_03771
- - Name: conda:bioconda
- Entry: sra-tools
+- Name: bio.tools
+Entry: sra-tools
+Name: SciCrunch
Repository: https://github.com/ncbi/sra-tools.git
Repository-Browse: https://github.com/ncbi/sra-tools
=====================================
debian/watch
=====================================
@@ -1,3 +1,10 @@
-version=4
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/ncbi/sra-tools/tags .*/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+Version: 5
+
+Repack-Suffix: +dfsg
+Debian-Version-Mangle: s/\+dfsg//g
+Compression: xz
+Filename-Mangle: s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%
+Dversion-Mangle: s/\+(dfsg|ds|debian|repack)(\d*)$//
+Template: GitHub
+Owner: ncbi
+Project: sra-tools
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/b50b336bfc29838cc3c2d3c3d53e1a4916509462...ad18e223b2ad30355e3ef99c76b1b45dff4e9ba9
--
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/b50b336bfc29838cc3c2d3c3d53e1a4916509462...ad18e223b2ad30355e3ef99c76b1b45dff4e9ba9
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