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debian/changelog
View file @ 2b2906a3
aegean (0.15.2+dfsg-2) unstable; urgency=medium
[ Andreas Tille ]
* Fix and adjust upstream metadata.
[ Steffen Moeller ]
* Fix EDAM annotations.
[ Sascha Steinbiss ]
* Update Uploader email address.
* Use debhelper 11.
* Use secure d/copyright format link.
* Bump Standards-Version.
* Update Vcs-* fields with Salsa addresses.
* Replace priority extra with optional.
* Remove unnecessary Testsuite field.
* Drop unused patch files.
* Drop -dbg package.
* Fix naming of lintian override.
-- Sascha Steinbiss <satta@debian.org> Wed, 04 Jul 2018 18:20:29 +0200
aegean (0.15.2+dfsg-1) unstable; urgency=medium
* New upstream version.
......
debian/control
View file @ 2b2906a3
Source: aegean
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Sascha Steinbiss <sascha@steinbiss.name>
Uploaders: Sascha Steinbiss <satta@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
Build-Depends: debhelper (>= 11),
libcairo2-dev,
libgenometools0-dev,
python,
git
Standards-Version: 3.9.7
Testsuite: autopkgtest
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/aegean.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/aegean.git
Standards-Version: 4.1.4
Vcs-Browser: https://salsa.debian.org/med-team/aegean
Vcs-Git: https://salsa.debian.org/med-team/aegean.git
Homepage: http://standage.github.io/AEGeAn
Package: aegean
......@@ -27,15 +26,3 @@ Description: integrated genome analysis toolkit
Annotations. The toolkit includes a variety of analysis programs, e.g. for
comparing distinct sets of gene structure annotations (ParsEval), computation
of gene loci (LocusPocus) and more.
Package: aegean-dbg
Architecture: amd64 arm64 armel armhf i386 mipsel powerpc ppc64el s390x hurd-i386 kfreebsd-amd64 kfreebsd-i386 ppc64 x32
Section: debug
Priority: extra
Depends: ${shlibs:Depends},
${misc:Depends},
aegean (= ${binary:Version})
Description: integrated genome analysis toolkit, with debug symbols
This package contains debug information stripped from AEGeAn.
You may decide to install it to help identifying issues, typically
to help communication with upstream developers.
debian/copyright
View file @ 2b2906a3
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: aegean
Source: http://aegean.readthedocs.org/en/v0.10.2/license.html
Files-Excluded: data/share/vendor/jquery.js data/misc/amel-ogs-vs-ncbi-parseval-html/vendor/jquery.js data/share/vendor/jquery.dataTables.js data/misc/amel-ogs-vs-ncbi-parseval-html/vendor/jquery.dataTables.js data/share/vendor/mootools-core-1.3.2-full-nocompat-yc.js data/misc/amel-ogs-vs-ncbi-parseval-html/vendor/mootools-core-1.3.2-full-nocompat-yc.js data/share/vendor/mootools-more-1.3.2.1.js data/misc/amel-ogs-vs-ncbi-parseval-html/vendor/mootools-more-1.3.2.1.js
......
debian/patches/add_version deleted 100644 → 0
View file @ b59c9b6d
Description: Add_version
--- a/Makefile
+++ b/Makefile
@@ -99,47 +99,47 @@
$(AGN_OBJS): obj/%.o : src/core/%.c inc/core/%.h inc/core/AgnVersion.h
@- mkdir -p obj
@ echo "[compile $*]"
- @ $(CC) $(CFLAGS) $(INCS) -c -o $@ $<
+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -c -o $@ $<
$(PE_EXE): src/ParsEval/parseval.c src/ParsEval/pe_options.c src/ParsEval/pe_utils.c src/ParsEval/pe_options.h src/ParsEval/pe_utils.h $(AGN_OBJS)
@ mkdir -p bin
@ echo "[compile ParsEval]"
- @ $(CC) $(CFLAGS) $(INCS) -I src/ParsEval -o $@ $(AGN_OBJS) src/ParsEval/parseval.c src/ParsEval/pe_options.c src/ParsEval/pe_utils.c $(LDFLAGS)
+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -I src/ParsEval -o $@ $(AGN_OBJS) src/ParsEval/parseval.c src/ParsEval/pe_options.c src/ParsEval/pe_utils.c $(LDFLAGS)
$(CN_EXE): src/canon-gff3.c $(AGN_OBJS)
@ mkdir -p bin
@ echo "[compile CanonGFF3]"
- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/canon-gff3.c $(LDFLAGS)
+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/canon-gff3.c $(LDFLAGS)
$(LP_EXE): src/locuspocus.c $(AGN_OBJS)
@ mkdir -p bin
@ echo "[compile LocusPocus]"
- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/locuspocus.c $(LDFLAGS)
+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/locuspocus.c $(LDFLAGS)
$(GV_EXE): src/gaeval.c $(AGN_OBJS)
@ mkdir -p bin
@ echo "[compile GAEVAL]"
- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/gaeval.c $(LDFLAGS)
+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/gaeval.c $(LDFLAGS)
$(XT_EXE): src/xtractore.c $(AGN_OBJS)
@ mkdir -p bin
@ echo "[compile Xtractore]"
- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/xtractore.c $(LDFLAGS)
+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/xtractore.c $(LDFLAGS)
$(RP_EXE): src/pmrna.c $(AGN_OBJS)
@ mkdir -p bin
@ echo "[compile $@]"
- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/pmrna.c $(LDFLAGS)
+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/pmrna.c $(LDFLAGS)
$(TD_EXE): src/tidygff3.c $(AGN_OBJS)
@ mkdir -p bin
@ echo "[compile $@]"
- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/tidygff3.c $(LDFLAGS)
+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/tidygff3.c $(LDFLAGS)
$(UT_EXE): test/unittests.c $(AGN_OBJS)
@ mkdir -p bin
@ echo "[compile unit tests]"
- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) test/unittests.c $(LDFLAGS)
+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) test/unittests.c $(LDFLAGS)
libaegean.a: $(AGN_OBJS)
@ echo "[create libaegean]"
debian/patches/remove_jquery deleted 100644 → 0
View file @ b59c9b6d
This diff is collapsed.
debian/patches/remove_mootools deleted 100644 → 0
View file @ b59c9b6d
This diff is collapsed.
debian/patches/sort_source_files deleted 100644 → 0
View file @ b59c9b6d
Description: Sort_source_files
--- a/Makefile
+++ b/Makefile
@@ -21,7 +21,7 @@
#----- Source, header, and object files -----#
# AEGeAn core class and module files
-AGN_SRCS=$(wildcard src/core/Agn*.c)
+AGN_SRCS=$(sort $(wildcard src/core/Agn*.c))
AGN_OBJS=$(patsubst src/core/%.c,obj/%.o,$(AGN_SRCS))
AGN_HDRS=$(patsubst src/core%.c,inc/core/%.h,$(AGN_SRCS))
debian/rules
View file @ 2b2906a3
......@@ -28,9 +28,6 @@ override_dh_auto_test:
override_dh_auto_install:
dh_auto_install -- 64bit=$(64BIT) prefix=$(DESTDIR)
override_dh_strip:
dh_strip --dbg-package=aegean-dbg
override_dh_installdocs:
cp $(CURDIR)/README.md $(CURDIR)/README
dh_installdocs
debian/source.lintian-overrides
View file @ 2b2906a3
# Upstream does not provide signed tarballs.
aegean source: debian-watch-may-check-gpg-signature
aegean source: debian-watch-does-not-check-gpg-signature