[med-svn] [Git][med-team/ea-utils][master] 5 commits: Update data
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Wed Aug 4 21:04:54 BST 2021
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 <shruti.sridhar99 at gmail.com> 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 <nilesh at debian.org> 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 <erik at q32.com>
2010 Illumina, Inc
License: MIT
-Files: debian/tests/data/*
-Copyright: NCBI
-License: PD
-
Files: razf.c
Copyright: 2008, Jue Ruan <ruanjue at gmail.com>, Heng Li <lh3 at sanger.ac.uk>
License: BSD-2-clause
@@ -64,6 +60,10 @@ Copyright: © 2014 Tim Booth <tbooth at ceh.ac.uk>
© 2015 Andreas Tille <tille at debian.org>
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 <nilesh at debian.org>
+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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20210804/42856276/attachment-0001.htm>
More information about the debian-med-commit
mailing list