[med-svn] [Git][med-team/libgclib][master] 4 commits: Lib builds now after excluding GBam.cpp from Makefile.am Its not really clear...
Andreas Tille
gitlab at salsa.debian.org
Thu Jun 13 15:53:57 BST 2019
Andreas Tille pushed to branch master at Debian Med / gclib
Commits:
70a4689c by Andreas Tille at 2019-06-13T14:35:13Z
Lib builds now after excluding GBam.cpp from Makefile.am Its not really clear what 'bam.h' is needed
- - - - -
0eed4119 by Andreas Tille at 2019-06-13T14:42:34Z
lib package and libdevel package - move source package name and salsa repository to libgclib
- - - - -
e79b8333 by Andreas Tille at 2019-06-13T14:45:00Z
Use d-shlibs
- - - - -
be9a73a2 by Andreas Tille at 2019-06-13T14:48:21Z
Fix d-shlibs install
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/patches/autoconf.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-gclib (0.11.2-1) UNRELEASED; urgency=medium
+libgclib (0.11.2-1) UNRELEASED; urgency=medium
* Initial release (Closes: #924582)
see https://salsa.debian.org/med-team/genome-code-lib
=====================================
debian/control
=====================================
@@ -1,25 +1,56 @@
-Source: gclib
+Source: libgclib
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 12~)
+Build-Depends: debhelper (>= 12~),
+ d-shlibs,
+ libgd-dev
Standards-Version: 4.3.0
-Vcs-Browser: https://salsa.debian.org/med-team/gclib
-Vcs-Git: https://salsa.debian.org/med-team/gclib.git
+Vcs-Browser: https://salsa.debian.org/med-team/libgclib
+Vcs-Git: https://salsa.debian.org/med-team/libgclib.git
Homepage: https://github.com/gpertea/gclib
-Package: gclib
+Package: libgclib-dev
Architecture: any
+Multi-Arch: same
+Section: libdevel
+Depends: libgclib0 (= ${binary:Version}),
+ ${misc:Depends}
+Description: header files for Genome Code Lib (GCLib)
+ This is an eclectic gathering of (mostly) C++ code which upstream used
+ for some bioinformatics projects. The main idea is to provide
+ lean code and efficient data structures, trying to avoid too many code
+ dependencies of heavy libraries while minimizing production cycles (and
+ this also implies a decent compile/build time -- looking at you,
+ bloated configure scripts and lengthy compile times of Boost code or
+ other heavy C++ template code..).
+ .
+ This code was gathered even before the C++ STL had been fully adopted as
+ a cross-platform "standard". Since STL by itself is a bit heavier for
+ most of the C++ needs, it is prefered to use simpler&leaner C++ classes
+ or templates for basic strings, containers, basic algorithms etc.
+ .
+ Header files of Genome Code Lib. It is mainly known for being
+ used by StringTie but with its own release cycle.
+
+Package: libgclib0
+Architecture: any
+Multi-Arch: same
+Section: libs
Depends: ${shlibs:Depends},
${misc:Depends}
-Description: Genomic C(++) library of reusable code for bioinformatics projects
- This is an eclectic gathering of (mostly) C++ code which used for
- some of my bioinformatics projects. The main idea is to provide lean
- code and efficient data structures, trying to avoid too many code
- dependencies of heavy libraries while minimizing production cycles.
+Description: C++ library to handle biological short sequence data
+ This is an eclectic gathering of (mostly) C++ code which upstream used
+ for some bioinformatics projects. The main idea is to provide
+ lean code and efficient data structures, trying to avoid too many code
+ dependencies of heavy libraries while minimizing production cycles (and
+ this also implies a decent compile/build time -- looking at you,
+ bloated configure scripts and lengthy compile times of Boost code or
+ other heavy C++ template code..).
.
This code was gathered even before the C++ STL had been fully adopted as
a cross-platform "standard". Since STL by itself is a bit heavier for
- most of my C++ needs, it is prefered to use simpler&leaner C++ classes
+ most of the C++ needs, it is prefered to use simpler&leaner C++ classes
or templates for basic strings, containers, basic algorithms etc.
=====================================
debian/patches/autoconf.patch
=====================================
@@ -4,7 +4,7 @@ Descriptions: Build proper libraries via automake
--- /dev/null
+++ b/Makefile.am
-@@ -0,0 +1,29 @@
+@@ -0,0 +1,32 @@
+lib_LTLIBRARIES = libgclib.la
+
+libgclibdir=$(includedir)
@@ -13,7 +13,6 @@ Descriptions: Build proper libraries via automake
+ GAlnExtend.cpp \
+ GapAssem.cpp \
+ GArgs.cpp \
-+ GBam.cpp \
+ GBase.cpp \
+ gcdb.cpp \
+ GCdbYank.cpp \
@@ -27,6 +26,10 @@ Descriptions: Build proper libraries via automake
+ GStr.cpp \
+ gtest.cpp \
+ GThreads.cpp
++
++# GBam.cpp # Exists but is not build by upstream Makefile
++# # Would need bam.h / sam.h
++
+libgclib_la_LDFLAGS = -version-info @LIB_VERSION@
+
+libgclib_la_CPPFLAGS = $(INCLUDES)
=====================================
debian/rules
=====================================
@@ -4,28 +4,20 @@
export LC_ALL=C.UTF-8
include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-# specified by <https://reproducible-builds.org/specs/source-date-epoch/>
-# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_CXXFLAGS_MAINT_APPEND = -Wall -pedantic -flto -fPIC
+export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed -Wl,-flto
%:
dh $@
-### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
-#override_dh_auto_test:
-#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-# do_stuff_for_testing
-#endif
-
-### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script
-#get-orig-source:
-# . debian/get-orig-source
+override_dh_install:
+ dh_install
+ d-shlibmove --commit \
+ --multiarch \
+ --devunversioned \
+ --exclude-la \
+ --movedev debian/tmp/usr/include usr \
+ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig \
+ debian/tmp/usr/lib/*/*.so
View it on GitLab: https://salsa.debian.org/med-team/libgclib/compare/345fe34c5285c792e969a66f195e0d5cffb5a325...be9a73a2bf6990889b574d6adf2ba8d3439d096e
--
View it on GitLab: https://salsa.debian.org/med-team/libgclib/compare/345fe34c5285c792e969a66f195e0d5cffb5a325...be9a73a2bf6990889b574d6adf2ba8d3439d096e
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