[med-svn] r19990 - in trunk/packages/minc/trunk/debian: . patches
Steven Michael Robbins
smr at moszumanska.debian.org
Sat Aug 22 20:52:11 UTC 2015
Author: smr
Date: 2015-08-22 20:52:10 +0000 (Sat, 22 Aug 2015)
New Revision: 19990
Added:
trunk/packages/minc/trunk/debian/patches/build-using-system-find-dot-cmake
trunk/packages/minc/trunk/debian/patches/series
Removed:
trunk/packages/minc/trunk/debian/index.html
trunk/packages/minc/trunk/debian/libminc-dev.doc-base
trunk/packages/minc/trunk/debian/patches/series
trunk/packages/minc/trunk/debian/watch
Modified:
trunk/packages/minc/trunk/debian/changelog
trunk/packages/minc/trunk/debian/control
trunk/packages/minc/trunk/debian/copyright
trunk/packages/minc/trunk/debian/rules
Log:
New version of minc libraries. Upstream has split the former minc sources into libminc and minc-tools. This repostiory is now tracking libminc only.
Modified: trunk/packages/minc/trunk/debian/changelog
===================================================================
--- trunk/packages/minc/trunk/debian/changelog 2015-08-22 20:15:15 UTC (rev 19989)
+++ trunk/packages/minc/trunk/debian/changelog 2015-08-22 20:52:10 UTC (rev 19990)
@@ -1,3 +1,11 @@
+libminc (2.3.00~2015-08-22-1) unstable; urgency=medium
+
+ * New upstream. Contains library source only. New minc-tools source
+ package will build minc-tools. Source tarball retrieved from github
+ master branch.
+
+ -- Steve M. Robbins <smr at debian.org> Sat, 22 Aug 2015 15:51:17 -0500
+
minc (2.2.00-6) unstable; urgency=medium
* Apply two patches fixing Mahem test issues. Thanks to Martin
Modified: trunk/packages/minc/trunk/debian/control
===================================================================
--- trunk/packages/minc/trunk/debian/control 2015-08-22 20:15:15 UTC (rev 19989)
+++ trunk/packages/minc/trunk/debian/control 2015-08-22 20:52:10 UTC (rev 19990)
@@ -1,12 +1,11 @@
-Source: minc
+Source: libminc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Steve M. Robbins <smr at debian.org>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
- autotools-dev,
- dh-autoreconf,
+ cmake (>= 2.8.5),
libnetcdf-dev,
zlib1g-dev,
texlive-latex-base,
@@ -14,31 +13,10 @@
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/minc/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/minc/trunk/
-Homepage: http://www.bic.mni.mcgill.ca/ServicesSoftware/HomePage
+Homepage: https://github.com/BIC-MNI/libminc
-Package: minc-tools
+Package: libminc2-3.0.0
Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- netcdf-bin,
- libgetopt-tabular-perl,
- libtext-format-perl,
- imagemagick
-Description: MNI medical image format tools
- This package contains tools to manipulate MINC files.
- .
- The Minc file format is a highly flexible medical image file format
- built on top of the NetCDF generalized data format. The format is
- simple, self-describing, extensible, portable and N-dimensional, with
- programming interfaces for both low-level data access and high-level
- volume manipulation. On top of the libraries is a suite of generic
- image-file manipulation tools. The format, libraries and tools are
- designed for use in a medical-imaging research environment: they are
- simple and powerful and make no attempt to provide a pretty interface
- to users.
-
-Package: libminc2-3
-Architecture: any
Multi-Arch: same
Section: libs
Depends: ${shlibs:Depends},
@@ -63,7 +41,7 @@
Architecture: any
Section: libdevel
Depends: ${misc:Depends},
- libminc2-3 (= ${binary:Version}),
+ libminc2-3.0.0 (= ${binary:Version}),
libnetcdf-dev,
libhdf5-dev
Conflicts: libminc0-dev
Modified: trunk/packages/minc/trunk/debian/copyright
===================================================================
--- trunk/packages/minc/trunk/debian/copyright 2015-08-22 20:15:15 UTC (rev 19989)
+++ trunk/packages/minc/trunk/debian/copyright 2015-08-22 20:52:10 UTC (rev 19990)
@@ -1,8 +1,8 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: MINC
+Upstream-Name: LIBMINC
Upstream-Contact: http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-development
Source: http://packages.bic.mni.mcgill.ca/tgz/
- https://github.com/BIC-MNI/libminc/releases
+ https://github.com/BIC-MNI/libminc/
Files: *
Deleted: trunk/packages/minc/trunk/debian/index.html
===================================================================
--- trunk/packages/minc/trunk/debian/index.html 2015-08-22 20:15:15 UTC (rev 19989)
+++ trunk/packages/minc/trunk/debian/index.html 2015-08-22 20:52:10 UTC (rev 19990)
@@ -1,38 +0,0 @@
-<html>
-<head>
-<title>MINC Documentation</title>
-</head>
-
-<body>
-
-<h1>MINC Library Documentation</h1>
-
-The MINC library is used to deal with large files typically encountered
-in medical imaging. A
-<a href="prog_guide.ps.gz">programmer's guide</a>
-and a
-<a href="prog_ref.ps.gz">programmer's reference manual</a>
-are available.
-
-<p> The <a href="volume_io.ps.gz">volume_io library</a>, also included
-in the MINC package, provides a simpler programming interface to MINC.
-</p>
-
-<h1>Additional Links</h1>
-
-<p>For other tools that work well with MINC, check
-out the <a href="http://www.bic.mni.mcgill.ca/software/">MNI Brain
-Imaging Centre software toolbox</a>.
-</p>
-
-<p>There are two mailing lists for MINC: <a
-href="http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users">minc
-users</a> and <a
-href="http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development">minc
-development</a>.
-</p>
-
-<hr>
-<address></address>
-<!-- hhmts start -->Last modified: Sat Dec 20 09:27:53 EST 2003 <!-- hhmts end -->
-</body> </html>
Deleted: trunk/packages/minc/trunk/debian/libminc-dev.doc-base
===================================================================
--- trunk/packages/minc/trunk/debian/libminc-dev.doc-base 2015-08-22 20:15:15 UTC (rev 19989)
+++ trunk/packages/minc/trunk/debian/libminc-dev.doc-base 2015-08-22 20:52:10 UTC (rev 19990)
@@ -1,15 +0,0 @@
-Document: minc
-Title: MINC Medical Image Format Library Reference
-Author: Peter Neelin
-Abstract: The Minc file format is a highly flexible medical image file format.
- Minc version 1 is built on top of the NetCDF generalized data format.
- Minc version 2 is built on top of the HDF data format. This library
- handles both formats. In each case the format is
- simple, self-describing, extensible, portable and N-dimensional, with
- programming interfaces for both low-level data access and high-level
- volume manipulation.
-Section: Science/Biology
-
-Format: HTML
-Index: /usr/share/doc/libminc-dev/index.html
-Files: /usr/share/doc/libminc-dev/index.html
Added: trunk/packages/minc/trunk/debian/patches/build-using-system-find-dot-cmake
===================================================================
--- trunk/packages/minc/trunk/debian/patches/build-using-system-find-dot-cmake (rev 0)
+++ trunk/packages/minc/trunk/debian/patches/build-using-system-find-dot-cmake 2015-08-22 20:52:10 UTC (rev 19990)
@@ -0,0 +1,23 @@
+Author: Steve Robbins <smr at debian.org>
+Last-Changed: Sat Aug 22 14:06:02 CDT 2015
+Forwarded-Upstream: No
+Description: Build using system findpackage.cmake files
+
+The sources contain an older copy of FindNETCDF.cmake.
+We delete that in debian/rules to use the system-supplied
+version, but also require this patch so that the newer
+variable HDF5_C_LIBRARIES is used.
+
+
+--- libminc-2.3.00~2015-08-22.orig/CMakeLists.txt
++++ libminc-2.3.00~2015-08-22/CMakeLists.txt
+@@ -60,6 +59,9 @@
+ # external packages
+ FIND_PACKAGE(ZLIB REQUIRED)
+ FIND_PACKAGE(HDF5 REQUIRED)
++
++ set(HDF5_LIBRARY ${HDF5_C_LIBRARIES})
++
+ ELSE(NOT LIBMINC_EXTERNALLY_CONFIGURED)
+ #TODO: set paths for HDF5 etc
+ ENDIF(NOT LIBMINC_EXTERNALLY_CONFIGURED)
Deleted: trunk/packages/minc/trunk/debian/patches/series
===================================================================
--- trunk/packages/minc/trunk/debian/patches/series 2015-08-22 20:15:15 UTC (rev 19989)
+++ trunk/packages/minc/trunk/debian/patches/series 2015-08-22 20:52:10 UTC (rev 19990)
@@ -1,8 +0,0 @@
-maxpathlen.patch
-makefile.patch
-01_mincedit-sensible-viewer.diff
-acrnema-version.patch
-pod_fix.diff
-clang.patch
-fix-crash-filename-null-voxel-loop.patch
-fix-crash-filename-null.patch
Added: trunk/packages/minc/trunk/debian/patches/series
===================================================================
--- trunk/packages/minc/trunk/debian/patches/series (rev 0)
+++ trunk/packages/minc/trunk/debian/patches/series 2015-08-22 20:52:10 UTC (rev 19990)
@@ -0,0 +1 @@
+build-using-system-find-dot-cmake
Modified: trunk/packages/minc/trunk/debian/rules
===================================================================
--- trunk/packages/minc/trunk/debian/rules 2015-08-22 20:15:15 UTC (rev 19989)
+++ trunk/packages/minc/trunk/debian/rules 2015-08-22 20:52:10 UTC (rev 19990)
@@ -1,49 +1,25 @@
#! /usr/bin/make -f
-%:
- dh $@ --with autoreconf --with autotools_dev
+ARCH = $(shell dpkg-architecture -qDEB_TARGET_MULTIARCH)
-ARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH)
-# Tests are buggy; disable test on sparc
-ifeq ($(ARCH),sparc)
- DEB_BUILD_OPTIONS += nocheck
-endif
+%:
+ dh $@
-ifneq ($(wildcard /usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial/libhdf5.so),)
- export DEB_CPPFLAGS_MAINT_APPEND := -I/usr/include/hdf5/serial
- export DEB_LDFLAGS_MAINT_APPEND := -Wl,-L/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial
-endif
+CMAKE_FLAGS = \
+ -DLIB_SUFFIX=/$(ARCH) \
+ -DBUILD_TESTING:BOOL=ON \
+ -DLIBMINC_BUILD_EZMINC_EXAMPLES:BOOL=ON \
+ -DLIBMINC_BUILD_SHARED_LIBS:BOOL=ON \
+ -DLIBMINC_MINC1_SUPPORT:BOOL=OFF
-DEB_CONFIGURE_EXTRA_FLAGS = --enable-shared --enable-minc2 --enable-acr-nema CFLAGS="$(CFLAGS)"
-
-
override_dh_auto_configure:
- dh_auto_configure -- $(DEB_CONFIGURE_EXTRA_FLAGS)
+ rm -f cmake-modules/*HDF5*
+ dh_auto_configure -- $(CMAKE_FLAGS)
-ps_docs = doc/prog_ref.ps doc/prog_guide.ps volume_io/Documentation/volume_io.ps
-
-doc/prog_ref.ps doc/prog_guide.ps:
- $(MAKE) -C doc docs
-
-volume_io/Documentation/volume_io.ps:
- $(MAKE) -C volume_io/Documentation docs
-
-override_dh_install: $(ps_docs)
- # minc-tools
- rm -f debian/tmp/usr/bin/byte_swap
- rm -f debian/tmp/usr/bin/extract
- rm -f debian/tmp/usr/bin/acr_test
- rm -f debian/tmp/usr/bin/dicom_test
- dh_install -pminc-tools --autodest debian/tmp/usr/bin
- dh_install -pminc-tools --autodest debian/tmp/usr/share/man
- dh_link -pminc-tools \
- /usr/share/man/man1/voxeltoworld.1 \
- /usr/share/man/man1/worldtovoxel.1
- # libminc2-3
- dh_install -plibminc2-3 --autodest debian/tmp/usr/lib/*/lib*.so.*
- # libminc-dev
+override_dh_install:
+ dh_install -plibminc2-3.0.0 --autodest debian/tmp/usr/lib/*/lib*.so.*
dh_install -plibminc-dev --autodest debian/tmp/usr/lib/*/lib*.so
- dh_install -plibminc-dev --autodest debian/tmp/usr/lib/*/lib*.a
- dh_install -plibminc-dev --autodest debian/tmp/usr/include
- dh_installdocs -plibminc-dev $(ps_docs) debian/index.html
+ dh_install -plibminc-dev debian/tmp/usr/lib/*/*.cmake /usr/lib/$(ARCH)/cmake/minc
+ dh_install -plibminc-dev --autodest debian/tmp/usr/include
+
Deleted: trunk/packages/minc/trunk/debian/watch
===================================================================
--- trunk/packages/minc/trunk/debian/watch 2015-08-22 20:15:15 UTC (rev 19989)
+++ trunk/packages/minc/trunk/debian/watch 2015-08-22 20:52:10 UTC (rev 19990)
@@ -1,2 +0,0 @@
-version=3
-http://packages.bic.mni.mcgill.ca/tgz/ minc-(.*)\.tar\.gz
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