Browse Source

ap/threeB: Removed.

current-20191101
Damien Goutte-Gattat 2 years ago
parent
commit
d1d361bd1d
  1. 12
      ap/threeB/slack-desc
  2. 1
      ap/threeB/threeB-1.1.tar.gz.sha1
  3. 131
      ap/threeB/threeB.SlackBuild
  4. 17
      l/gvars/gvars-3.0-fltk-includes.diff
  5. 1
      l/gvars/gvars-3.0.tar.bz2.sha1
  6. 122
      l/gvars/gvars.SlackBuild
  7. 12
      l/gvars/slack-desc
  8. 1
      l/libcvd/libcvd-20150407.tar.gz.sha1
  9. 122
      l/libcvd/libcvd.SlackBuild
  10. 12
      l/libcvd/slack-desc
  11. 1
      l/toon/TooN-2.2.tar.xz.sha1
  12. 12
      l/toon/slack-desc
  13. 118
      l/toon/toon.SlackBuild

12
ap/threeB/slack-desc

@ -1,12 +0,0 @@
|-----handy-ruler-------------------------------------------------------|
threeB: threeB (3B microscopy analysis software=
threeB:
threeB: Bayesian analysis of blinking and bleaching, or 3B microscopy, is a
threeB: method which analyses data in which many overloapping fluorophores
threeB: undergo bleaching and blinking events, giving the structure at
threeB: enhanced resolution. By using a Hidden Markov Model (HMM), it allows
threeB: useful information to be obtained from data that would be impossible
threeB: to analyse with standard localisation analysis techniques.
threeB:
threeB:
threeB:

1
ap/threeB/threeB-1.1.tar.gz.sha1

@ -1 +0,0 @@
91b6463613caeafd4cddc677a11c71095d2e67d3 threeB-1.1.tar.gz

131
ap/threeB/threeB.SlackBuild

@ -1,131 +0,0 @@
#!/bin/bash
# Build script for Slackware
# Copyright (C) 2013,2016 Damien Goutte-Gattat
#
# Redistribution and use of this script, with or without modifications,
# is permitted provided that the following conditions are met:
#
# 1. Redistributions of this script must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# THIS SOFTWARE IS PROVIDED BY THE AUTHOR AS IS'' AND ANY EXPRESS OR
# IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,
# INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
# HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
# STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
# IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#
# Contact: Damien Goutte-Gattat <dgouttegattat@incenp.org>
#
# Latest threeB sourcecode is available at:
# <http://www.coxphysics.com/3b/index.html>.
#
# Depends: l/tag, l/gvars, l/libcvd, l/libatlas
# Recommends: xap/fiji
# Source package infos
NAMESRC=${NAMESRC:-threeB}
VERSION=${VERSION:-1.1}
ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION.tar.gz}
WGET=${WGET:-http://www.coxphysics.com/3b/$ARCHIVE}
# Build infos
NAMEPKG=${NAMEPKG:-threeB}
BUILD=${BUILD:-2GGD}
ARCH=${ARCH:-$(uname -m | sed 's/^i.86$/i486/;s/^arm.*/arm/')}
JOBS=${JOBS:-1}
EXT=${EXT:-txz}
# Directories
TMP=${TMP:-/tmp}
OUT=${OUT:-$TMP/build}
PKG=${PKG:-$OUT/$NAMEPKG}
CWD=$(pwd)
IMAGEJ=${IMAGEJ:-/usr/lib/fiji/plugins}
set -e # Quit if a command returns non-zero
# Sanity checks
if [ $UID -eq 0 ]; then
echo "You should NOT run this script as ROOT!"
exit 1
fi
if [ ! -d $TMP ]; then
echo "$TMP does not exists or is not a directory!"
exit 1
fi
# Compilation flags
LIBDIRSUFFIX=""
case "$ARCH" in
i?86)
CPUOPT="-O2 -march=$ARCH -mtune=i686"
;;
x86_64)
CPUOPT="-O2 -fPIC"
LIBDIRSUFFIX="64"
;;
*)
CPUOPT="-O2"
;;
esac
# Get and verify the source archive
if [ ! -r $ARCHIVE ]; then
wget -c -O $ARCHIVE.part "$WGET"
mv $ARCHIVE.part $ARCHIVE
fi
sha1sum -c $ARCHIVE.sha1
NAME=$(tar ft $ARCHIVE | head -n 1 | cut -d / -f 1)
# Compile
cd $TMP
echo "Building $ARCHIVE..."
tar xf $CWD/$ARCHIVE
cd $NAME
CFLAGS=$CPUOPT \
CXXFLAGS=$CPUOPT \
LIBS="-lcblas -lf77blas -latlas" \
./configure \
--prefix=/usr \
--libdir=/usr/lib$LIBDIRSUFFIX \
--with-imagej=/usr/lib/fiji/jars/ij-1.50e.jar \
--with-jni=/usr/lib64/jdk1.8.0_91/include
make -j $JOBS prog
make -j $JOBS plugin DYNAMIC_PLUGIN=1
# Install
install -D -m 755 -s multispot5_headless $PKG/usr/bin/multispot5
install -D -m 644 three_B.jar $PKG$IMAGEJ/ThreeB/three_B.jar
if [ "x$ARCH" == xx86_64 ]; then
install -m 755 -s libthreeB_jni.so $PKG$IMAGEJ/ThreeB/libthreeB_jni_64.so
else
install -m 755 -s libthreeB_jni.so $PKG$IMAGEJ/ThreeB/libthreeB_jni_32.so
fi
# Install the documentation
mkdir -p $PKG/usr/doc/$NAME
install -m 644 README LICENSE $PKG/usr/doc/$NAME
# Copy slack-desc file
install -D -m 644 $CWD/slack-desc $PKG/install/slack-desc
# Package the tree
cd $PKG
mkdir -p $OUT
PACKAGING="
chown root:root . -R
/sbin/makepkg -l y -c n $OUT/$NAMEPKG-$VERSION-$ARCH-$BUILD.$EXT
rm -rf $PKG
rm -rf $TMP/$NAME
"
if type -p fakeroot ; then
echo "$PACKAGING" | fakeroot
else
su -c "$PACKAGING"
fi

17
l/gvars/gvars-3.0-fltk-includes.diff

@ -1,17 +0,0 @@
diff --git a/gvars-3.0.orig/src/GUI_Fltk.cc b/gvars-3.0/src/GUI_Fltk.cc
index ccc0ee7..91e254e 100644
--- a/gvars-3.0.orig/src/GUI_Fltk.cc
+++ b/gvars-3.0/src/GUI_Fltk.cc
@@ -37,9 +37,9 @@
#include <FL/Fl_Widget.H>
#include <FL/Fl_Button.H>
#include <FL/Fl_Check_Button.H>
-#include <Fl/Fl_Value_Slider.H>
-#include <Fl/Fl_Value_Input.H>
-#include <Fl/Fl_Box.H>
+#include <FL/Fl_Value_Slider.H>
+#include <FL/Fl_Value_Input.H>
+#include <FL/Fl_Box.H>
#define POLL_UPDATE 1

1
l/gvars/gvars-3.0.tar.bz2.sha1

@ -1 +0,0 @@
b7a9e2f0c90ad600f54e27c88bd9093eb3b59031 gvars-3.0.tar.bz2

122
l/gvars/gvars.SlackBuild

@ -1,122 +0,0 @@
#!/bin/bash
# Build script for Slackware
# Copyright (C) 2013 Damien Goutte-Gattat
#
# Redistribution and use of this script, with or without modifications,
# is permitted provided that the following conditions are met:
#
# 1. Redistributions of this script must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# THIS SOFTWARE IS PROVIDED BY THE AUTHOR AS IS'' AND ANY EXPRESS OR
# IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,
# INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
# HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
# STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
# IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#
# Contact: Damien Goutte-Gattat <dgouttegattat@incenp.org>
#
# Latest gvars sourcecode is available at:
# <http://www.edwardrosten.com/cvd/gvars3.html>.
#
# Recommends: l/fltk, l/toon
# Source package infos
NAMESRC=${NAMESRC:-gvars}
VERSION=${VERSION:-3.0}
ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION.tar.bz2}
WGET=${WGET:-http://www.edwardrosten.com/cvd/$ARCHIVE}
# Build infos
NAMEPKG=${NAMEPKG:-gvars}
BUILD=${BUILD:-1GGD}
ARCH=${ARCH:-$(uname -m | sed 's/^i.86$/i486/;s/^arm.*/arm/')}
JOBS=${JOBS:-1}
EXT=${EXT:-txz}
# Directories
TMP=${TMP:-/tmp}
OUT=${OUT:-$TMP/build}
PKG=${PKG:-$OUT/$NAMEPKG}
CWD=$(pwd)
set -e # Quit if a command returns non-zero
# Sanity checks
if [ $UID -eq 0 ]; then
echo "You should NOT run this script as ROOT!"
exit 1
fi
if [ ! -d $TMP ]; then
echo "$TMP does not exists or is not a directory!"
exit 1
fi
# Compilation flags
LIBDIRSUFFIX=""
case "$ARCH" in
i?86)
CPUOPT="-O2 -march=$ARCH -mtune=i686"
;;
x86_64)
CPUOPT="-O2 -fPIC"
LIBDIRSUFFIX="64"
;;
*)
CPUOPT="-O2"
;;
esac
# Get and verify the source archive
if [ ! -r $ARCHIVE ]; then
wget -c -O $ARCHIVE.part "$WGET"
mv $ARCHIVE.part $ARCHIVE
fi
sha1sum -c $ARCHIVE.sha1
NAME=$(tar ft $ARCHIVE | head -n 1 | cut -d / -f 1)
# Compile
cd $TMP
echo "Building $ARCHIVE..."
tar xf $CWD/$ARCHIVE
cd $NAME
patch -p 2 < $CWD/gvars-3.0-fltk-includes.diff
CFLAGS=$CPUOPT \
CXXFLAGS=$CPUOPT \
./configure \
--prefix=/usr \
--libdir=/usr/lib$LIBDIRSUFFIX
make -j $JOBS
make install DESTDIR=$PKG
# Strip binaries
find $PKG | xargs file | grep "ELF \(32\|64\)-bit LSB" | cut -d : -f 1 | \
xargs strip --strip-unneeded 2> /dev/null
# Install the documentation
mkdir -p $PKG/usr/doc/$NAME
install -m 644 Authors LICENSE $PKG/usr/doc/$NAME
# Copy slack-desc file
install -D -m 644 $CWD/slack-desc $PKG/install/slack-desc
# Package the tree
cd $PKG
mkdir -p $OUT
PACKAGING="
chown root:root . -R
/sbin/makepkg -l y -c n $OUT/$NAMEPKG-$VERSION-$ARCH-$BUILD.$EXT
rm -rf $PKG
rm -rf $TMP/$NAME
"
if type -p fakeroot ; then
echo "$PACKAGING" | fakeroot
else
su -c "$PACKAGING"
fi

12
l/gvars/slack-desc

@ -1,12 +0,0 @@
|-----handy-ruler--------------------------------------------------------|
gvars: gvars (configuration system library)
gvars:
gvars: GVars is a configuration library.
gvars:
gvars:
gvars:
gvars:
gvars:
gvars:
gvars:
gvars:

1
l/libcvd/libcvd-20150407.tar.gz.sha1

@ -1 +0,0 @@
aa22f6aee72c6aca5a2086fe57b3bf2439122469 libcvd-20150407.tar.gz

122
l/libcvd/libcvd.SlackBuild

@ -1,122 +0,0 @@
#!/bin/bash
# Build script for Slackware
# Copyright (C) 2013,2016 Damien Goutte-Gattat
#
# Redistribution and use of this script, with or without modifications,
# is permitted provided that the following conditions are met:
#
# 1. Redistributions of this script must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# THIS SOFTWARE IS PROVIDED BY THE AUTHOR AS IS'' AND ANY EXPRESS OR
# IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,
# INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
# HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
# STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
# IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#
# Contact: Damien Goutte-Gattat <dgouttegattat@incenp.org>
#
# Latest libcvd sourcecode is available at:
# <http://www.edwardrosten.com/cvd/index.html>.
#
# Recommends: l/toon, xap/ffmpeg
# Source package infos
NAMESRC=${NAMESRC:-libcvd}
VERSION=${VERSION:-20150407}
ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION.tar.gz}
WGET=${WGET:-http://www.edwardrosten.com/cvd/$ARCHIVE}
# Build infos
NAMEPKG=${NAMEPKG:-libcvd}
BUILD=${BUILD:-1GGD}
ARCH=${ARCH:-$(uname -m | sed 's/^i.86$/i486/;s/^arm.*/arm/')}
JOBS=${JOBS:-1}
EXT=${EXT:-txz}
# Directories
TMP=${TMP:-/tmp}
OUT=${OUT:-$TMP/build}
PKG=${PKG:-$OUT/$NAMEPKG}
CWD=$(pwd)
set -e # Quit if a command returns non-zero
# Sanity checks
if [ $UID -eq 0 ]; then
echo "You should NOT run this script as ROOT!"
exit 1
fi
if [ ! -d $TMP ]; then
echo "$TMP does not exists or is not a directory!"
exit 1
fi
# Compilation flags
LIBDIRSUFFIX=""
case "$ARCH" in
i?86)
CPUOPT="-O2 -march=$ARCH -mtune=i686"
;;
x86_64)
CPUOPT="-O2 -fPIC"
LIBDIRSUFFIX="64"
;;
*)
CPUOPT="-O2"
;;
esac
# Get and verify the source archive
if [ ! -r $ARCHIVE ]; then
wget -c -O $ARCHIVE.part "$WGET"
mv $ARCHIVE.part $ARCHIVE
fi
sha1sum -c $ARCHIVE.sha1
NAME=$(tar ft $ARCHIVE | head -n 1 | cut -d / -f 1)
# Compile
cd $TMP
echo "Building $ARCHIVE..."
tar xf $CWD/$ARCHIVE
cd $NAME
CFLAGS=$CPUOPT \
CXXFLAGS=$CPUOPT \
./configure \
--prefix=/usr \
--libdir=/usr/lib$LIBDIRSUFFIX \
--enable-gpl
make -j $JOBS
make install DESTDIR=$PKG
# Strip binaries
find $PKG | xargs file | grep "ELF \(32\|64\)-bit LSB" | cut -d : -f 1 | \
xargs strip --strip-unneeded 2> /dev/null
# Install the documentation
mkdir -p $PKG/usr/doc/$NAME
install -m 644 Authors LICENSE TODO $PKG/usr/doc/$NAME
# Copy slack-desc file
install -D -m 644 $CWD/slack-desc $PKG/install/slack-desc
# Package the tree
cd $PKG
mkdir -p $OUT
PACKAGING="
chown root:root . -R
/sbin/makepkg -l y -c n $OUT/$NAMEPKG-$VERSION-$ARCH-$BUILD.$EXT
rm -rf $PKG
rm -rf $TMP/$NAME
"
if type -p fakeroot ; then
echo "$PACKAGING" | fakeroot
else
su -c "$PACKAGING"
fi

12
l/libcvd/slack-desc

@ -1,12 +0,0 @@
|-----handy-ruler-------------------------------------------------------|
libcvd: libcvd (computer vision library)
libcvd:
libcvd: libCVD is a very portable and high performance C++ library for
libcvd: computer vision, image, and video processing.
libcvd:
libcvd:
libcvd:
libcvd:
libcvd:
libcvd:
libcvd:

1
l/toon/TooN-2.2.tar.xz.sha1

@ -1 +0,0 @@
dc65657c3f4165d87742e28de754ce5f7daf3e57 TooN-2.2.tar.xz

12
l/toon/slack-desc

@ -1,12 +0,0 @@
|-----handy-ruler---------------------------------------------------------|
toon: toon (object-oriented numeric library)
toon:
toon: TooN is a C++ numerics library which is designed to operate efficiently
toon: on large number of small matrices, and provides easy access to a
toon: number of algorithms including matrix decompositions and optimizations.
toon:
toon: TooN is type generic and will work very well.
toon:
toon:
toon:
toon:

118
l/toon/toon.SlackBuild

@ -1,118 +0,0 @@
#!/bin/bash
# Build script for Slackware
# Copyright (C) 2013,2016 Damien Goutte-Gattat
#
# Redistribution and use of this script, with or without modifications,
# is permitted provided that the following conditions are met:
#
# 1. Redistributions of this script must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# THIS SOFTWARE IS PROVIDED BY THE AUTHOR AS IS'' AND ANY EXPRESS OR
# IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,
# INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
# HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
# STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
# IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#
# Contact: Damien Goutte-Gattat <dgouttegattat@incenp.org>
#
# Latest TooN sourcecode is available at:
# <http://www.edwardrosten.com/cvd/toon.html>.
#
# Recommends: l/atlas
# Source package infos
NAMESRC=${NAMESRC:-TooN}
VERSION=${VERSION:-2.2}
ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION.tar.xz}
WGET=${WGET:-http://www.edwardrosten.com/cvd/$ARCHIVE}
# Build infos
NAMEPKG=${NAMEPKG:-toon}
BUILD=${BUILD:-1GGD}
ARCH=${ARCH:-$(uname -m | sed 's/^i.86$/i486/;s/^arm.*/arm/')}
JOBS=${JOBS:-1}
EXT=${EXT:-txz}
# Directories
TMP=${TMP:-/tmp}
OUT=${OUT:-$TMP/build}
PKG=${PKG:-$OUT/$NAMEPKG}
CWD=$(pwd)
set -e # Quit if a command returns non-zero
# Sanity checks
if [ $UID -eq 0 ]; then
echo "You should NOT run this script as ROOT!"
exit 1
fi
if [ ! -d $TMP ]; then
echo "$TMP does not exists or is not a directory!"
exit 1
fi
# Compilation flags
LIBDIRSUFFIX=""
case "$ARCH" in
i?86)
CPUOPT="-O2 -march=$ARCH -mtune=i686"
;;
x86_64)
CPUOPT="-O2 -fPIC"
LIBDIRSUFFIX="64"
;;
*)
CPUOPT="-O2"
;;
esac
# Get and verify the source archive
if [ ! -r $ARCHIVE ]; then
wget -c -O $ARCHIVE.part "$WGET"
mv $ARCHIVE.part $ARCHIVE
fi
sha1sum -c $ARCHIVE.sha1
NAME=$(tar ft $ARCHIVE | head -n 1 | cut -d / -f 1)
# Compile
cd $TMP
echo "Building $ARCHIVE..."
tar xf $CWD/$ARCHIVE
cd $NAME
CFLAGS=$CPUOPT \
CXXFLAGS=$CPUOPT \
./configure \
--prefix=/usr \
--libdir=/usr/lib$LIBDIRSUFFIX
make install DESTDIR=$PKG
# Install the documentation
mkdir -p $PKG/usr/doc/$NAME
install -m 644 COPYING README TODO $PKG/usr/doc/$NAME
doxygen
cp -r html $PKG/usr/doc/$NAME
# Copy slack-desc file
install -D -m 644 $CWD/slack-desc $PKG/install/slack-desc
# Package the tree
cd $PKG
mkdir -p $OUT
PACKAGING="
chown root:root . -R
/sbin/makepkg -l y -c n $OUT/$NAMEPKG-$VERSION-$ARCH-$BUILD.$EXT
rm -rf $PKG
rm -rf $TMP/$NAME
"
if type -p fakeroot ; then
echo "$PACKAGING" | fakeroot
else
su -c "$PACKAGING"
fi
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