Nilesh Patra pushed to branch master at Debian Med / ea-utils
Commits: bff3a9d2 by Nilesh Patra at 2021-08-04T19:35:17+00:00 Update data - - - - - cd3e6335 by Nilesh Patra at 2021-08-05T01:09:11+05:30 Fix copyright - - - - - 86435aa8 by Nilesh Patra at 2021-08-05T01:13:05+05:30 Drop useless B-D on r-cran-hmisc - - - - - 2fccc1b2 by Nilesh Patra at 2021-08-05T01:22:46+05:30 Make build cross-buildable - - - - - 72e243e9 by Nilesh Patra at 2021-08-05T01:27:51+05:30 Interim changelog entry - - - - - 6 changed files: - debian/changelog - debian/control - debian/copyright - + debian/patches/cross.patch - debian/patches/series - debian/tests/data/data.fastq.gz Changes: ===================================== debian/changelog ===================================== @@ -1,13 +1,22 @@ ea-utils (1.1.2+dfsg-7) UNRELEASED; urgency=medium + [ Shruti Sridhar ] * Team Upload. - * Add test data - * Add get-test-data script * Add autopkgtests - * Install docs - * Update hardening options - - -- Shruti Sridhar <[email protected]> Wed, 04 Aug 2021 20:21:48 +0530 + - Add test data in d/tests/data + - Add d/tests/get-test-data script to fetch test data via script, + and update the same when needed + - d/docs: Install test README and d/tests/run-unit-test script + - d/example: Install test data as example + - debian/source/include-binaries: Allow compressed test data binary + to be included in source + * d/p/hardening.patch: Update hardening options + + [ Nilesh Patra ] + * d/control: Drop useless B-D on r-cran-hmisc + * d/p/cross.patch: Fix compiler variable to get package cross-building + + -- Nilesh Patra <[email protected]> Thu, 05 Aug 2021 01:22:52 +0530 ea-utils (1.1.2+dfsg-6) unstable; urgency=medium ===================================== debian/control ===================================== @@ -9,7 +9,6 @@ Build-Depends: debhelper-compat (= 13), zlib1g-dev, libgsl-dev, libsparsehash-dev, - r-cran-hmisc Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/ea-utils Vcs-Git: https://salsa.debian.org/med-team/ea-utils.git ===================================== debian/copyright ===================================== @@ -14,10 +14,6 @@ Copyright: © 2011 Erik Aronesty <[email protected]> 2010 Illumina, Inc License: MIT -Files: debian/tests/data/* -Copyright: NCBI -License: PD - Files: razf.c Copyright: 2008, Jue Ruan <[email protected]>, Heng Li <[email protected]> License: BSD-2-clause @@ -64,6 +60,10 @@ Copyright: © 2014 Tim Booth <[email protected]> © 2015 Andreas Tille <[email protected]> License: MIT +Files: debian/tests/data/* +Copyright: NCBI +License: PD + License: MIT Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal ===================================== debian/patches/cross.patch ===================================== @@ -0,0 +1,59 @@ +Description: Pass right compiler name to CXX variable +Author: Nilesh Patra <[email protected]> +Last-Update: 2021-08-05 +--- a/Makefile ++++ b/Makefile +@@ -1,7 +1,7 @@ + # + # $Id: Makefile 670 2013-12-13 16:47:07Z earonesty $ + +-CC=g++ ++CXX=g++ + PREFIX?=/usr + BINDIR?=$(PREFIX)/bin + CFLAGS?=-O3 -I. +@@ -64,21 +64,21 @@ + cp $< $@ + + %: %.c fastq-lib.cpp fastq-lib.h +- $(CC) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp -o $@ $< $(LDFLAGS) ++ $(CXX) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp -o $@ $< $(LDFLAGS) + + %: %.cpp fastq-lib.cpp fastq-lib.h +- $(CC) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp -o $@ $< $(LDFLAGS) ++ $(CXX) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp -o $@ $< $(LDFLAGS) + + + %: %.c gcModel.c gcModel.h +- $(CC) $(CFLAGS) $(CPPFLAGS) gcModel.c -o $@ $< $(LDFLAGS) ++ $(CXX) $(CFLAGS) $(CPPFLAGS) gcModel.c -o $@ $< $(LDFLAGS) + + %: %.cpp gcModel.c gcModel.h +- $(CC) $(CFLAGS) $(CPPFLAGS) gcModel.c -o $@ $< $(LDFLAGS) ++ $(CXX) $(CFLAGS) $(CPPFLAGS) gcModel.c -o $@ $< $(LDFLAGS) + + # why the libbam.a doesn't work? not sure... *.o works + sam-stats: sam-stats.cpp fastq-lib.h +- $(CC) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp $< -lbam -lz -lpthread -o $@ $(LDFLAGS) ++ $(CXX) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp $< -lbam -lz -lpthread -o $@ $(LDFLAGS) + + samtools/libbam.a: samtools/*.c samtools/*.h + cd samtools && make libbam.a +@@ -87,14 +87,14 @@ + ifeq ($(OS),Windows_NT) + echo varcall: not supported yet + else +- $(CC) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp tidx/tidx-lib.cpp -o $@ $< -lgsl -lgslcblas $(LDFLAGS) ++ $(CXX) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp tidx/tidx-lib.cpp -o $@ $< -lgsl -lgslcblas $(LDFLAGS) + endif + + fastq-stats: fastq-stats.cpp fastq-lib.cpp gcModel.c +- $(CC) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp gcModel.c -o $@ $< $(LDFLAGS) ++ $(CXX) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp gcModel.c -o $@ $< $(LDFLAGS) + + bam-filter: bam-filter.cpp +- $(CC) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp -o $@ $< -lbamtools $(LDFLAGS) ++ $(CXX) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp -o $@ $< -lbamtools $(LDFLAGS) + + clean: + rm -f *.o $(BIN) ===================================== debian/patches/series ===================================== @@ -1,3 +1,4 @@ makefile.patch hardening.patch name-space-conflict.patch +cross.patch ===================================== debian/tests/data/data.fastq.gz ===================================== Binary files a/debian/tests/data/data.fastq.gz and b/debian/tests/data/data.fastq.gz differ View it on GitLab: https://salsa.debian.org/med-team/ea-utils/-/compare/4d6e32f2cdc86df737f9cbf39a819f5e11a8fb3d...72e243e9015abeb9cbc77accc7501f671ef4e9bf -- View it on GitLab: https://salsa.debian.org/med-team/ea-utils/-/compare/4d6e32f2cdc86df737f9cbf39a819f5e11a8fb3d...72e243e9015abeb9cbc77accc7501f671ef4e9bf You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
