[med-svn] [Git][med-team/htsjdk][master] 2 commits: Drop the unused Build-Depends on scala-library
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Oct 2 12:00:59 BST 2026
Andreas Tille pushed to branch master at Debian Med / htsjdk
Commits:
9242d2f5 by Juan Manuel Méndez Rey at 2026-10-02T00:59:28+02:00
Drop the unused Build-Depends on scala-library
- - - - -
fac98817 by Juan Manuel Méndez Rey at 2026-10-02T10:31:12+02:00
d/copyright: fix the holders and licences found by licensecheck/lrc
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/lrc.config
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+htsjdk (5.0.0+dfsg-2) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Drop the unused Build-Depends on scala-library. Nothing in the build
+ or the tests compiles Scala any more (upstream removed the Scala
+ build in 4.x, and deleted the leftover Scala tests in
+ https://github.com/samtools/htsjdk/pull/1847). This takes htsjdk out
+ of the scala-asm autoremoval chain (#1142168).
+ * d/copyright: CRAMBAIIndexer.java carries both the EMBL-EBI Apache-
+ 2.0 and the Broad Institute MIT notices; declare the Apache-2.0
+ Gradle wrapper scripts and the hts-specs test data (Genome Research
+ Ltd. and others, with the BSD-3-clause and MIT exceptions); complete
+ the ISC licence text. Add debian/lrc.config for the remaining name-
+ only differences.
+
+ -- Juan Manuel Méndez Rey <juan.mendezr at proton.me> Fri, 02 Oct 2026 00:59:21 +0200
+
htsjdk (5.0.0+dfsg-1) unstable; urgency=medium
* New upstream version 5.0.0+dfsg
=====================================
debian/control
=====================================
@@ -26,8 +26,7 @@ Build-Depends: default-jdk,
junit4,
libcommons-lang3-java,
libjimfs-java,
- samtools <!nocheck>,
- scala-library
+ samtools <!nocheck>
Standards-Version: 4.7.4
Vcs-Browser: https://salsa.debian.org/med-team/htsjdk
Vcs-Git: https://salsa.debian.org/med-team/htsjdk.git
=====================================
debian/copyright
=====================================
@@ -16,7 +16,54 @@ License: Apache-2.0
Files: src/main/java/htsjdk/samtools/CRAMBAIIndexer.java
Copyright: 2013-2016 EMBL-EBI
-License: Apache-2.0 or Expat
+ 2014 The Broad Institute
+License: Apache-2.0 and Expat
+Comment:
+ The file carries both notices: the EMBL-EBI Apache-2.0 header and the
+ Broad Institute MIT licence.
+
+Files: src/main/java/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.java
+Copyright: 2004-2009 The Broad Institute
+ 2003 Jan Wigginton, Goncalo Abecasis
+License: Expat
+Comment:
+ hwCalculate() is credited to Wigginton and Abecasis (2003), the authors
+ of the exact SNP-HWE test; the file is distributed by the Broad Institute
+ under the MIT licence.
+
+Files: gradlew
+ gradlew.bat
+Copyright: 2015-2021 the original authors
+License: Apache-2.0
+Comment: The Gradle wrapper scripts (the wrapper jar is excluded).
+
+Files: src/test/resources/htsjdk/hts-specs/*
+Copyright: 2019-2023 Genome Research Ltd.
+ 2021 John Marshall
+ EBI (European Bioinformatics Institute)
+ 2022-2024 Daniel Cameron
+License: Apache-2.0
+Comment:
+ Test data from the GA4GH hts-specs test suite; the LICENSE file of each
+ subdirectory gives the holders and the Apache-2.0 licence. The vcf
+ LICENSE notes that complexfile_passed_000.vcf looks like a subset of 1000
+ Genomes data, which may instead be under the 1000 Genomes terms (freely
+ available, Fort Lauderdale Agreement).
+
+Files: src/test/resources/htsjdk/hts-specs/test/cram/codecs/*
+Copyright: 2019-2023 Genome Research Ltd.
+License: Apache-2.0 or BSD-3-clause
+Comment:
+ "jointly available under the Apache 2.0 license and the BSD license"
+ (from Staden io_lib and htscodecs).
+
+Files: src/test/resources/htsjdk/hts-specs/test/SAMtags/parse_mm.pl
+Copyright: 2020 Genome Research Ltd.
+License: BSD-3-clause
+
+Files: src/test/resources/htsjdk/hts-specs/test/sam/compare_sam.pl
+Copyright: 2013-2018 Genome Research Ltd.
+License: Expat
Files: src/main/java/htsjdk/samtools/ChainedDownsamplingIterator.java
src/main/java/htsjdk/samtools/ConstantMemoryDownsamplingIterator.java
@@ -312,3 +359,40 @@ License: ISC
Permission to use, copy, modify, and/or distribute this software for any
purpose with or without fee is hereby granted, provided that the above
copyright notice and this permission notice appear in all copies.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+ WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+ MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+ ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+ WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+ ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
+ OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+
+License: BSD-3-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are
+ met:
+ .
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ .
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ .
+ 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+ Institute nor the names of its contributors may be used to endorse or
+ promote products derived from this software without specific prior
+ written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS"
+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE
+ LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ POSSIBILITY OF SUCH DAMAGE.
=====================================
debian/lrc.config
=====================================
@@ -0,0 +1,19 @@
+# licenserecon configuration for htsjdk
+#
+# Aliases (d/copyright name | licensecheck name), pure name differences:
+W3C-Software | W3C-19980720
+Apache-2.0 and Public-Domain | Apache-2.0 and/or public-domain
+# CRAMBAIIndexer.java carries both notices; licensecheck reports only the
+# first one.
+Apache-2.0 and Expat | Apache-2.0
+
+# The licence statement of the codecs test data (it names both licences;
+# licensecheck reads only Apache-2.0).
+src/test/resources/htsjdk/hts-specs/test/cram/codecs/LICENSE
+
+# A lock file listing the licences of the validation tool's dependencies
+# (data that mentions licences, not a licence of the file).
+validation/pixi.lock
+
+# This file is scanned too.
+debian/lrc.config
View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/3bf1c1609f8bf38b2e44d7c7bdae8eb765939cbc...fac98817582110c8cbcbcf69fdb669bff1537b45
--
View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/3bf1c1609f8bf38b2e44d7c7bdae8eb765939cbc...fac98817582110c8cbcbcf69fdb669bff1537b45
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