Package: release.debian.org
Severity: normal
User: release.debian....@packages.debian.org
Usertags: freeze-exception
Please unblock package cmtk
Upstream reported that users reported missing some binaries which were
referenced in a recent paper describing methodologies implemented in cmtk. The
reason was missing build depends on libfftw3-dev. -2 revision of the package
just adds those build-depends and adds an explicit cmake option to build with
support for libfftw3 functionality. As debdiff shows there are additional
patches under debian/patches -- but those are applied only when building
backports for NeuroDebian repository. I am also attaching debdiff on the
.changes to show now added missing binaries.
unblock cmtk/2.2.2-2
Thanks in advance
-- System Information:
Debian Release: wheezy/sid
APT prefers testing
APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100,
'stable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 3.2.0-3-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_US, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash
[The following lists of changes regard files as different if they have
different names, permissions or owners.]
Files in second .changes but not in first
-----------------------------------------
-rw-r--r-- root/root /usr/share/doc/cmtk/upstream
-rw-r--r-- root/root /usr/share/man/man1/cmtk-detect_adni_phantom.1.gz
-rw-r--r-- root/root
/usr/share/man/man1/cmtk-detect_spheres_matched_filter.1.gz
-rwxr-xr-x root/root /usr/lib/cmtk/bin/detect_adni_phantom
-rwxr-xr-x root/root /usr/lib/cmtk/bin/detect_spheres_matched_filter
Control files: lines which differ (wdiff format)
------------------------------------------------
Depends: libbz2-1.0, libc6 (>= 2.7), libcharls1, libdcmtk2 (>= 3.6.0),
{+libfftw3-3,+} libgcc1 (>= 1:4.1.1), libgomp1 (>= 4.2.1), libmxml1, libpng12-0
(>= 1.2.13-4), libqtcore4 (>= 4:4.6.1), libqtgui4 (>= 4:4.5.3), libsqlite3-0
(>= 3.5.9), libstdc++6 (>= 4.6), libtiff4 (>> 3.9.5-3~), zlib1g (>= 1:1.1.4)
Installed-Size: [-22969-] {+23343+}
Version: [-2.2.2-1-] {+2.2.2-2+}
diff -Nru cmtk-2.2.2/debian/changelog cmtk-2.2.2/debian/changelog
--- cmtk-2.2.2/debian/changelog 2012-06-18 16:01:56.000000000 -0400
+++ cmtk-2.2.2/debian/changelog 2012-07-20 09:47:02.000000000 -0400
@@ -1,3 +1,14 @@
+cmtk (2.2.2-2) unstable; urgency=low
+
+ * Adding libfftw3-dev into build-depends and adding
+ CMTK_USE_FFTW:BOOL=ON for cmake. Should make detect_adni_phantom
+ referenced in a publication available.
+ - for backports to older releases (e.g. squeeze) compatibility patch
+ up_compat_older_fftw is provided and added to corresponding series
+ * Added debian/upstream with a publication reference (added to debian/docs)
+
+ -- Yaroslav Halchenko <deb...@onerussian.com> Wed, 18 Jul 2012 13:03:08 -0400
+
cmtk (2.2.2-1) unstable; urgency=low
* Fresh upstream release
diff -Nru cmtk-2.2.2/debian/control cmtk-2.2.2/debian/control
--- cmtk-2.2.2/debian/control 2012-06-18 16:01:56.000000000 -0400
+++ cmtk-2.2.2/debian/control 2012-07-20 09:47:02.000000000 -0400
@@ -10,6 +10,7 @@
zlib1g-dev | libz-dev,
libdcmtk2-dev | libdcmtk1-dev | libdcmtk-dev,
libbz2-dev,
+ libfftw3-dev,
liblzma-dev,
libqt4-dev, qt4-qmake,
libpng-dev,
diff -Nru cmtk-2.2.2/debian/docs cmtk-2.2.2/debian/docs
--- cmtk-2.2.2/debian/docs 2012-06-18 16:01:56.000000000 -0400
+++ cmtk-2.2.2/debian/docs 2012-07-20 09:47:02.000000000 -0400
@@ -1 +1,2 @@
README.txt
+debian/upstream
diff -Nru cmtk-2.2.2/debian/patches/series-lucid cmtk-2.2.2/debian/patches/series-lucid
--- cmtk-2.2.2/debian/patches/series-lucid 1969-12-31 19:00:00.000000000 -0500
+++ cmtk-2.2.2/debian/patches/series-lucid 2012-07-20 09:47:02.000000000 -0400
@@ -0,0 +1 @@
+up_compat_older_fftw
diff -Nru cmtk-2.2.2/debian/patches/series-maverick cmtk-2.2.2/debian/patches/series-maverick
--- cmtk-2.2.2/debian/patches/series-maverick 1969-12-31 19:00:00.000000000 -0500
+++ cmtk-2.2.2/debian/patches/series-maverick 2012-07-20 09:47:02.000000000 -0400
@@ -0,0 +1 @@
+up_compat_older_fftw
diff -Nru cmtk-2.2.2/debian/patches/series-natty cmtk-2.2.2/debian/patches/series-natty
--- cmtk-2.2.2/debian/patches/series-natty 2012-06-18 16:01:56.000000000 -0400
+++ cmtk-2.2.2/debian/patches/series-natty 2012-07-20 09:47:02.000000000 -0400
@@ -1 +1,2 @@
deb_noCharLS
+up_compat_older_fftw
diff -Nru cmtk-2.2.2/debian/patches/series-oneiric cmtk-2.2.2/debian/patches/series-oneiric
--- cmtk-2.2.2/debian/patches/series-oneiric 2012-06-18 16:01:56.000000000 -0400
+++ cmtk-2.2.2/debian/patches/series-oneiric 2012-07-20 09:47:02.000000000 -0400
@@ -1 +1,2 @@
deb_noCharLS
+up_compat_older_fftw
diff -Nru cmtk-2.2.2/debian/patches/series-squeeze cmtk-2.2.2/debian/patches/series-squeeze
--- cmtk-2.2.2/debian/patches/series-squeeze 1969-12-31 19:00:00.000000000 -0500
+++ cmtk-2.2.2/debian/patches/series-squeeze 2012-07-20 09:47:02.000000000 -0400
@@ -0,0 +1 @@
+up_compat_older_fftw
diff -Nru cmtk-2.2.2/debian/patches/up_compat_older_fftw cmtk-2.2.2/debian/patches/up_compat_older_fftw
--- cmtk-2.2.2/debian/patches/up_compat_older_fftw 1969-12-31 19:00:00.000000000 -0500
+++ cmtk-2.2.2/debian/patches/up_compat_older_fftw 2012-07-20 09:47:02.000000000 -0400
@@ -0,0 +1,55 @@
+From 0584a2224f924b5e89ba39c173f9a2c53d95b9cb Mon Sep 17 00:00:00 2001
+From: torsten_at_home <torsten_at_home@42a5c34f-2066-0410-bec5-ba365beb4995>
+Date: Fri, 20 Jul 2012 04:04:00 +0000
+Subject: [PATCH] FIX: fall back to lower-level allocation API, as convenience
+ functions not available in less-than-most-recent FFTW
+ version
+
+git-svn-id: https://www.nitrc.org/svn/cmtk/trunk@4458 42a5c34f-2066-0410-bec5-ba365beb4995
+---
+ .../cmtkSphereDetectionBipolarMatchedFilterFFT.cxx | 4 ++--
+ ...mtkSphereDetectionNormalizedBipolarMatchedFilterFFT.cxx | 12 ++++++------
+ 2 files changed, 8 insertions(+), 8 deletions(-)
+
+diff --git a/libs/Segmentation/cmtkSphereDetectionBipolarMatchedFilterFFT.cxx b/libs/Segmentation/cmtkSphereDetectionBipolarMatchedFilterFFT.cxx
+index dc8d9ff..9469cda 100644
+--- a/libs/Segmentation/cmtkSphereDetectionBipolarMatchedFilterFFT.cxx
++++ b/libs/Segmentation/cmtkSphereDetectionBipolarMatchedFilterFFT.cxx
+@@ -35,8 +35,8 @@ cmtk::SphereDetectionBipolarMatchedFilterFFT::SphereDetectionBipolarMatchedFilte
+ m_ImageDims( image.m_Dims ),
+ m_PixelSize( image.m_Delta )
+ {
+- this->m_ImageFT = fftw_alloc_complex( this->m_NumberOfPixels );
+- this->m_FilterFT = fftw_alloc_complex( this->m_NumberOfPixels );
++ this->m_ImageFT = static_cast<fftw_complex*>( fftw_malloc( sizeof( fftw_complex ) * this->m_NumberOfPixels ) );
++ this->m_FilterFT = static_cast<fftw_complex*>( fftw_malloc( sizeof( fftw_complex ) * this->m_NumberOfPixels ) );
+
+ this->m_PlanFilter = fftw_plan_dft_3d( this->m_ImageDims[2], this->m_ImageDims[1], this->m_ImageDims[0], this->m_FilterFT, this->m_FilterFT, FFTW_FORWARD, FFTW_ESTIMATE );
+ this->m_PlanBackward = fftw_plan_dft_3d( this->m_ImageDims[2], this->m_ImageDims[1], this->m_ImageDims[0], this->m_FilterFT, this->m_FilterFT, FFTW_BACKWARD, FFTW_ESTIMATE );
+diff --git a/libs/Segmentation/cmtkSphereDetectionNormalizedBipolarMatchedFilterFFT.cxx b/libs/Segmentation/cmtkSphereDetectionNormalizedBipolarMatchedFilterFFT.cxx
+index 63f101f..3322d65 100644
+--- a/libs/Segmentation/cmtkSphereDetectionNormalizedBipolarMatchedFilterFFT.cxx
++++ b/libs/Segmentation/cmtkSphereDetectionNormalizedBipolarMatchedFilterFFT.cxx
+@@ -37,13 +37,13 @@ cmtk::SphereDetectionNormalizedBipolarMatchedFilterFFT::SphereDetectionNormalize
+ m_SphereRadius( 0 ),
+ m_MarginWidth( -1 )
+ {
+- this->m_ImageFT = fftw_alloc_complex( this->m_NumberOfPixels );
+- this->m_ImageSquareFT = fftw_alloc_complex( this->m_NumberOfPixels );
++ this->m_ImageFT = static_cast<fftw_complex*>( fftw_malloc( sizeof( fftw_complex ) * this->m_NumberOfPixels ) );
++ this->m_ImageSquareFT = static_cast<fftw_complex*>( fftw_malloc( sizeof( fftw_complex ) * this->m_NumberOfPixels ) );
+
+- this->m_FilterFT = fftw_alloc_complex( this->m_NumberOfPixels );
+- this->m_FilterSquareFT = fftw_alloc_complex( this->m_NumberOfPixels );
+- this->m_FilterMaskFT = fftw_alloc_complex( this->m_NumberOfPixels );
+- this->m_FilterMaskFT2 = fftw_alloc_complex( this->m_NumberOfPixels );
++ this->m_FilterFT = static_cast<fftw_complex*>( fftw_malloc( sizeof( fftw_complex ) * this->m_NumberOfPixels ) );
++ this->m_FilterSquareFT = static_cast<fftw_complex*>( fftw_malloc( sizeof( fftw_complex ) * this->m_NumberOfPixels ) );
++ this->m_FilterMaskFT = static_cast<fftw_complex*>( fftw_malloc( sizeof( fftw_complex ) * this->m_NumberOfPixels ) );
++ this->m_FilterMaskFT2 = static_cast<fftw_complex*>( fftw_malloc( sizeof( fftw_complex ) * this->m_NumberOfPixels ) );
+
+ this->m_PlanFilter = fftw_plan_dft_3d( this->m_ImageDims[2], this->m_ImageDims[1], this->m_ImageDims[0], this->m_FilterFT, this->m_FilterFT, FFTW_FORWARD, FFTW_ESTIMATE );
+ this->m_PlanFilterSquare = fftw_plan_dft_3d( this->m_ImageDims[2], this->m_ImageDims[1], this->m_ImageDims[0], this->m_FilterSquareFT, this->m_FilterSquareFT, FFTW_FORWARD, FFTW_ESTIMATE );
+--
+1.7.10.4
+
diff -Nru cmtk-2.2.2/debian/rules cmtk-2.2.2/debian/rules
--- cmtk-2.2.2/debian/rules 2012-06-18 16:01:56.000000000 -0400
+++ cmtk-2.2.2/debian/rules 2012-07-20 09:47:02.000000000 -0400
@@ -43,6 +43,7 @@
-DCMTK_BUILD_ZLIB:BOOL=OFF \
-DCMTK_ROOT_PATH_SRI24:PATH=/usr/share/data/sri24-atlas \
-DCMTK_USE_DCMTK:BOOL=ON \
+ -DCMTK_USE_FFTW:BOOL=ON \
-DCMTK_USE_QT:BOOL=ON \
-DCMTK_USE_SMP:BOOL=ON \
-DCMTK_USE_SQLITE:BOOL=ON \
diff -Nru cmtk-2.2.2/debian/upstream cmtk-2.2.2/debian/upstream
--- cmtk-2.2.2/debian/upstream 1969-12-31 19:00:00.000000000 -0500
+++ cmtk-2.2.2/debian/upstream 2012-07-20 09:47:02.000000000 -0400
@@ -0,0 +1,8 @@
+Reference:
+ Author: T. Rohlfing
+ Title: User Guide to The Computational Morphometry Toolkit
+ Journal: The Insight Journal
+ Year: 2009
+ URL: http://hdl.handle.net/10380/3140
+ eprint: http://www.midasjournal.org/download/viewpdf/706/3/download
+
