[med-svn] [khmer] 01/01: fix copyright files statement; clean up overrides
Michael Crusoe
misterc-guest at moszumanska.debian.org
Fri Jul 31 18:21:39 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository khmer.
commit 8b604e05260a0bd7d7bb15e713efa36c2db76f2d
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Fri Jul 31 07:12:22 2015 -0700
fix copyright files statement; clean up overrides
fix liboxli SO version
fix misc paths
---
debian/copyright | 2 +-
debian/doc-base | 4 ++--
debian/khmer-common.lintian-overrides | 1 +
debian/khmer.lintian-overrides | 22 ++++++++++++++++++++
debian/liboxli-dev.install | 2 --
debian/liboxli1.install | 3 ++-
debian/lintian-overrides | 14 -------------
debian/patches/install-prefix | 39 +++++++++++++++++++++++++++++++++++
debian/rules | 2 +-
9 files changed, 68 insertions(+), 21 deletions(-)
diff --git a/debian/copyright b/debian/copyright
index ae0177b..46a71ee 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -32,7 +32,7 @@ Copyright: (c) 2002, Paul Mensonides
2002, The Trustees of Indiana University
License: boost-1.0
-Files: third-party/smhasher
+Files: third-party/smhasher/*
Copyright: none.
License: public-domain
Quoting from the file header: "MurmurHash3 was written by Austin Appleby,
diff --git a/debian/doc-base b/debian/doc-base
index 11809af..5d2678f 100644
--- a/debian/doc-base
+++ b/debian/doc-base
@@ -13,5 +13,5 @@ Abstract: in-memory DNA sequence kmer counting, filtering & graph traversal
Section: Science/Biology
Format: html
-Files: /usr/share/doc/khmer/html/*
-Index: /usr/share/doc/khmer/html/index.html
+Files: /usr/share/doc/khmer-common/html/*
+Index: /usr/share/doc/khmer-common/html/index.html
diff --git a/debian/khmer-common.lintian-overrides b/debian/khmer-common.lintian-overrides
new file mode 100644
index 0000000..5686645
--- /dev/null
+++ b/debian/khmer-common.lintian-overrides
@@ -0,0 +1 @@
+khmer-common: extra-license-file usr/share/doc/khmer-common/html/_sources/LICENSE.txt
diff --git a/debian/khmer.lintian-overrides b/debian/khmer.lintian-overrides
new file mode 100644
index 0000000..2b3b18f
--- /dev/null
+++ b/debian/khmer.lintian-overrides
@@ -0,0 +1,22 @@
+# These files are unchanged files from upstream tarball. There is no problem for a reproducible build
+khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.gz
+khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.truncated.gz
+khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.gz
+khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/goodversion-k12.ht.gz
+khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fa.gz
+khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fq.gz
+khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/test-abund-read-2.fa.gz
+khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/test-reads.fq.gz
+
+# The test data are provided in different compression methods intentionally to test different compression methods
+# Since they are small anyway there is no reason to work around this
+khmer: duplicated-compressed-file usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.bz2
+khmer: duplicated-compressed-file usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.gz
+khmer: duplicated-compressed-file usr/lib/python3/dist-packages/khmer/tests/test-data/goodversion-k12.ht.gz
+khmer: duplicated-compressed-file usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fa.bz2
+khmer: duplicated-compressed-file usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fa.gz
+khmer: duplicated-compressed-file usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fq.bz2
+khmer: duplicated-compressed-file usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fq.gz
+khmer: duplicated-compressed-file usr/lib/python3/dist-packages/khmer/tests/test-data/test-abund-read-2.fa.bz2
+khmer: duplicated-compressed-file usr/lib/python3/dist-packages/khmer/tests/test-data/test-abund-read-2.fa.gz
+khmer: duplicated-compressed-file usr/lib/python3/dist-packages/khmer/tests/test-data/test-empty.fa.bz2
diff --git a/debian/liboxli-dev.install b/debian/liboxli-dev.install
index 786b4d4..78e99a1 100755
--- a/debian/liboxli-dev.install
+++ b/debian/liboxli-dev.install
@@ -1,6 +1,4 @@
#!/usr/bin/dh-exec
-lib/liboxli.so usr/lib/${DEB_HOST_MULTIARCH}
-lib/liboxli.so.2 usr/lib/${DEB_HOST_MULTIARCH}
lib/liboxli.a usr/lib/${DEB_HOST_MULTIARCH}
lib/oxli.pc usr/lib/${DEB_HOST_MULTIARCH}/pkgconfig
# NB: we install the headers to the oxli subdir.
diff --git a/debian/liboxli1.install b/debian/liboxli1.install
index 3bec701..950db6f 100755
--- a/debian/liboxli1.install
+++ b/debian/liboxli1.install
@@ -1,2 +1,3 @@
#!/usr/bin/dh-exec
-lib/liboxli.so.2.0~rc2+dfsg usr/lib/${DEB_HOST_MULTIARCH}
+lib/liboxli.so usr/lib/${DEB_HOST_MULTIARCH}
+lib/liboxli.so.1 usr/lib/${DEB_HOST_MULTIARCH}
diff --git a/debian/lintian-overrides b/debian/lintian-overrides
deleted file mode 100644
index 76ab46b..0000000
--- a/debian/lintian-overrides
+++ /dev/null
@@ -1,14 +0,0 @@
-# This licence is apart of upstream's documentation
-khmer: extra-license-file usr/share/doc/khmer/html/_sources/LICENSE.txt
-
-# These files are unchanged files from upstream tarball. There is no problem for a reproducible build
-khmer: package-contains-timestamped-gzip usr/lib/python2.7/dist-packages/khmer/tests/test-data/100-reads.fq.gz
-khmer: package-contains-timestamped-gzip usr/lib/python2.7/dist-packages/khmer/tests/test-data/100-reads.fq.truncated.gz
-khmer: package-contains-timestamped-gzip usr/lib/python2.7/dist-packages/khmer/tests/test-data/goodversion-k12.ht.gz
-khmer: package-contains-timestamped-gzip usr/lib/python2.7/dist-packages/khmer/tests/test-data/random-20-a.fa.gz
-khmer: package-contains-timestamped-gzip usr/lib/python2.7/dist-packages/khmer/tests/test-data/random-20-a.fq.gz
-khmer: package-contains-timestamped-gzip usr/lib/python2.7/dist-packages/khmer/tests/test-data/test-abund-read-2.fa.gz
-
-# The test data are provided in different compression methods intentionally to test different compression methods
-# Since they are small anyway there is no reason to work around this
-khmer: duplicated-compressed-file usr/lib/python2.7/dist-packages/khmer/tests/test-data/*
diff --git a/debian/patches/install-prefix b/debian/patches/install-prefix
index 56745d2..41f3a97 100644
--- a/debian/patches/install-prefix
+++ b/debian/patches/install-prefix
@@ -9,3 +9,42 @@
### NOTE: No user-serviceable parts below this line! ###
+@@ -118,24 +118,20 @@
+ VERSION = $(shell ./get_version.py)
+ endif
+
+-MAJOR_VERSION = $(shell echo $(VERSION) | sed -e 's/^\([^-\.]*\)\.\([^-\.]*\).*/\1/')
+-MINOR_VERSION = $(shell echo $(VERSION) | sed -e 's/^\([^-\.]*\)\.\([^-\.]*\).*/\2/')
+-
+-LIB_VERSION = $(MAJOR_VERSION).$(MINOR_VERSION)
++# The ABI version of liboxli
++LIBVERSION = 1
+
+ ifeq ($(shell uname), Darwin)
+ SHARED_EXT = dylib
+-SONAME = liboxli.$(SHARED_EXT).$(MAJOR_VERSION)
+-SONAME_FLAGS = -install_name $(PREFIX)/lib/$(SONAME) -compatibility_version $(MAJOR_VERSION) -current_version $(LIB_VERSION)
++SONAME = liboxli.$(SHARED_EXT).$(LIBVERSION)
++SONAME_FLAGS = -install_name $(PREFIX)/lib/$(SONAME) -current_version $(LIBVERSION)
+ else
+ SHARED_EXT = so
+-SONAME = liboxli.$(SHARED_EXT).$(MAJOR_VERSION)
++SONAME = liboxli.$(SHARED_EXT).$(LIBVERSION)
+ SONAME_FLAGS = -Wl,-soname=$(SONAME)
+ endif
+
+-# The ABI version of liboxli
+-LIBVERSION = 1
+-LIBKHMERSO=liboxli.$(SHARED_EXT).$(LIB_VERSION)
++LIBKHMERSO=liboxli.$(SHARED_EXT)
+
+ CXXFLAGS += -DVERSION=$(VERSION)
+
+@@ -270,7 +266,6 @@
+ $(LIBKHMERSO): $(LIBKHMER_OBJS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) $(SONAME_FLAGS) -shared -o $@ $^
+ ln -sf $(LIBKHMERSO) $(SONAME)
+- ln -sf $(SONAME) liboxli.$(SHARED_EXT)
+
+ liboxli.a: $(LIBKHMER_OBJS)
+ ar rcs $@ $^
diff --git a/debian/rules b/debian/rules
index 8f8ed38..710071d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -36,7 +36,7 @@ override_dh_auto_clean:
cd lib && $(MAKE) clean
override_dh_install:
- cd lib && $(MAKE) PREFIX=debian/tmp install
+ cd lib && $(MAKE) PREFIX=../debian/tmp install
dh_install
find debian/khmer -name .gitignore -delete
--
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