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commit 8b604e05260a0bd7d7bb15e713efa36c2db76f2d Author: Michael R. Crusoe <michael.cru...@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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit