[med-svn] r23740 - in trunk/packages/R/r-bioc-aroma.light/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Mon May 15 10:45:58 UTC 2017
Author: tille
Date: 2017-05-15 10:45:57 +0000 (Mon, 15 May 2017)
New Revision: 23740
Modified:
trunk/packages/R/r-bioc-aroma.light/trunk/debian/changelog
trunk/packages/R/r-bioc-aroma.light/trunk/debian/control
trunk/packages/R/r-bioc-aroma.light/trunk/debian/copyright
trunk/packages/R/r-bioc-aroma.light/trunk/debian/patches/remove_test_using_external_functions.patch
trunk/packages/R/r-bioc-aroma.light/trunk/debian/rules
Log:
Commit changes for 3.4.0-1
Modified: trunk/packages/R/r-bioc-aroma.light/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-aroma.light/trunk/debian/changelog 2017-05-12 18:42:13 UTC (rev 23739)
+++ trunk/packages/R/r-bioc-aroma.light/trunk/debian/changelog 2017-05-15 10:45:57 UTC (rev 23740)
@@ -1,3 +1,12 @@
+r-bioc-aroma.light (3.4.0-1) unstable; urgency=medium
+
+ * New upstream version
+ * Generic BioConductor homepage
+ * Switch to dh-r
+ * Versioned Build-Depends: r-cran-r.utils (>= 2.4.0)
+
+ -- Andreas Tille <tille at debian.org> Wed, 09 Nov 2016 09:40:07 +0100
+
r-bioc-aroma.light (3.2.0-1) unstable; urgency=medium
* New upstream version
Modified: trunk/packages/R/r-bioc-aroma.light/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-aroma.light/trunk/debian/control 2017-05-12 18:42:13 UTC (rev 23739)
+++ trunk/packages/R/r-bioc-aroma.light/trunk/debian/control 2017-05-15 10:45:57 UTC (rev 23740)
@@ -4,24 +4,22 @@
Section: gnu-r
Priority: optional
Build-Depends: debhelper (>= 9),
- cdbs,
+ dh-r,
r-base-dev,
r-cran-r.methodss3,
r-cran-matrixstats (>= 0.50.1),
- r-cran-r.utils
+ r-cran-r.utils (>= 2.4.0)
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-aroma.light/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-aroma.light/trunk/
-Homepage: http://bioconductor.org/packages/release/bioc/html/aroma.light.html
+Homepage: https://bioconductor.org/packages/aroma.light/
Package: r-bioc-aroma.light
Architecture: all
Depends: ${R:Depends},
${misc:Depends},
- r-cran-r.methodss3,
- r-cran-matrixstats (>= 0.50.1),
- r-cran-r.utils
-Suggests: r-cran-princurve
+Recommends: ${R:Recommends}
+Suggests: ${R:Suggests}
Description: BioConductor methods normalization and visualization of microarray data
This BioConductor module provides light-weight methods for
normalization and visualization of microarray data using only basic R
Modified: trunk/packages/R/r-bioc-aroma.light/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-aroma.light/trunk/debian/copyright 2017-05-12 18:42:13 UTC (rev 23739)
+++ trunk/packages/R/r-bioc-aroma.light/trunk/debian/copyright 2017-05-15 10:45:57 UTC (rev 23740)
@@ -1,14 +1,14 @@
-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: aroma.light
Upstream-Contact: Henrik Bengtsson <henrikb at braju.com>
-Source: http://www.bioconductor.org/packages/release/bioc/html/aroma.light.html
+Source: https://bioconductor.org/packages/aroma.light/
Files: *
-Copyright: 2006-2015 Henrik Bengtsson <henrikb at braju.com>
+Copyright: 2006-2016 Henrik Bengtsson <henrikb at braju.com>
License: GPL-2+
Files: debian/*
-Copyright: 2015 Andreas Tille <tille at debian.org>
+Copyright: 2015-2016 Andreas Tille <tille at debian.org>
License: GPL-2+
License: GPL-2+
Modified: trunk/packages/R/r-bioc-aroma.light/trunk/debian/patches/remove_test_using_external_functions.patch
===================================================================
--- trunk/packages/R/r-bioc-aroma.light/trunk/debian/patches/remove_test_using_external_functions.patch 2017-05-12 18:42:13 UTC (rev 23739)
+++ trunk/packages/R/r-bioc-aroma.light/trunk/debian/patches/remove_test_using_external_functions.patch 2017-05-15 10:45:57 UTC (rev 23740)
@@ -90,8 +90,83 @@
-
-} # for (zzz in 0)
-rm(zzz)
+--- a/tests/wpca.matrix.R
++++ /dev/null
+@@ -1,72 +0,0 @@
+-library("aroma.light")
+-
+-for (zzz in 0) {
+-
+-# This example requires plot3d() in R.basic [http://www.braju.com/R/]
+-if (!require(pkgName <- "R.basic", character.only=TRUE)) break
+-
+-# -------------------------------------------------------------
+-# A first example
+-# -------------------------------------------------------------
+-# Simulate data from the model y <- a + bx + eps(bx)
+-x <- rexp(1000)
+-a <- c(2,15,3)
+-b <- c(2,3,15)
+-bx <- outer(b,x)
+-eps <- apply(bx, MARGIN=2, FUN=function(x) rnorm(length(x), mean=0, sd=0.1*x))
+-y <- a + bx + eps
+-y <- t(y)
+-
+-# Add some outliers by permuting the dimensions for 1/3 of the observations
+-idx <- sample(1:nrow(y), size=1/3*nrow(y))
+-y[idx,] <- y[idx,c(2,3,1)]
+-
+-# Down-weight the outliers W times to demonstrate how weights are used
+-W <- 10
+-
+-# Plot the data with fitted lines at four different view points
+-N <- 4
+-theta <- seq(0,180,length=N)
+-phi <- rep(30, length.out=N)
+-
+-# Use a different color for each set of weights
+-col <- topo.colors(W)
+-
+-opar <- par(mar=c(1,1,1,1)+0.1)
+-layout(matrix(1:N, nrow=2, byrow=TRUE))
+-for (kk in seq(theta)) {
+- # Plot the data
+- plot3d(y, theta=theta[kk], phi=phi[kk])
+-
+- # First, same weights for all observations
+- w <- rep(1, length=nrow(y))
+-
+- for (ww in 1:W) {
+- # Fit a line using IWPCA through data
+- fit <- wpca(y, w=w, swapDirections=TRUE)
+-
+- # Get the first principal component
+- ymid <- fit$xMean
+- d0 <- apply(y, MARGIN=2, FUN=min) - ymid
+- d1 <- apply(y, MARGIN=2, FUN=max) - ymid
+- b <- fit$vt[1,]
+- y0 <- -b * max(abs(d0))
+- y1 <- b * max(abs(d1))
+- yline <- matrix(c(y0,y1), nrow=length(b), ncol=2)
+- yline <- yline + ymid
+-
+- points3d(t(ymid), col=col)
+- lines3d(t(yline), col=col)
+-
+- # Down-weight outliers only, because here we know which they are.
+- w[idx] <- w[idx]/2
+- }
+-
+- # Highlight the last one
+- lines3d(t(yline), col="red", lwd=3)
+-}
+-
+-par(opar)
+-
+-} # for (zzz in 0)
+-rm(zzz)
--- a/tests/iwpca.matrix.R
-+++ /dev/null
++++ b/tests/iwpca.matrix.R
@@ -1,76 +0,0 @@
-library("aroma.light")
-
@@ -133,10 +208,10 @@
-w <- rep(1, length(x)); w[idx] <- 0.8
-
-# ...and show all iterations too with different colors.
--maxIter <- c(seq(1,20,length=10),Inf)
+-maxIter <- c(seq(1,20,length.out=10),Inf)
-col <- topo.colors(length(maxIter))
-# Show the fitted value for every iteration
--for (ii in seq(along=maxIter)) {
+-for (ii in seq_along(maxIter)) {
- # Fit a line using IWPCA through data
- fit <- iwpca(y, w=w, maxIter=maxIter[ii], swapDirections=TRUE)
-
@@ -169,78 +244,3 @@
-
-} # for (zzz in 0)
-rm(zzz)
---- a/tests/wpca.matrix.R
-+++ /dev/null
-@@ -1,72 +0,0 @@
--library("aroma.light")
--
--for (zzz in 0) {
--
--# This example requires plot3d() in R.basic [http://www.braju.com/R/]
--if (!require(pkgName <- "R.basic", character.only=TRUE)) break
--
--# -------------------------------------------------------------
--# A first example
--# -------------------------------------------------------------
--# Simulate data from the model y <- a + bx + eps(bx)
--x <- rexp(1000)
--a <- c(2,15,3)
--b <- c(2,3,15)
--bx <- outer(b,x)
--eps <- apply(bx, MARGIN=2, FUN=function(x) rnorm(length(x), mean=0, sd=0.1*x))
--y <- a + bx + eps
--y <- t(y)
--
--# Add some outliers by permuting the dimensions for 1/3 of the observations
--idx <- sample(1:nrow(y), size=1/3*nrow(y))
--y[idx,] <- y[idx,c(2,3,1)]
--
--# Down-weight the outliers W times to demonstrate how weights are used
--W <- 10
--
--# Plot the data with fitted lines at four different view points
--N <- 4
--theta <- seq(0,180,length=N)
--phi <- rep(30, length.out=N)
--
--# Use a different color for each set of weights
--col <- topo.colors(W)
--
--opar <- par(mar=c(1,1,1,1)+0.1)
--layout(matrix(1:N, nrow=2, byrow=TRUE))
--for (kk in seq(theta)) {
-- # Plot the data
-- plot3d(y, theta=theta[kk], phi=phi[kk])
--
-- # First, same weights for all observations
-- w <- rep(1, length=nrow(y))
--
-- for (ww in 1:W) {
-- # Fit a line using IWPCA through data
-- fit <- wpca(y, w=w, swapDirections=TRUE)
--
-- # Get the first principal component
-- ymid <- fit$xMean
-- d0 <- apply(y, MARGIN=2, FUN=min) - ymid
-- d1 <- apply(y, MARGIN=2, FUN=max) - ymid
-- b <- fit$vt[1,]
-- y0 <- -b * max(abs(d0))
-- y1 <- b * max(abs(d1))
-- yline <- matrix(c(y0,y1), nrow=length(b), ncol=2)
-- yline <- yline + ymid
--
-- points3d(t(ymid), col=col)
-- lines3d(t(yline), col=col)
--
-- # Down-weight outliers only, because here we know which they are.
-- w[idx] <- w[idx]/2
-- }
--
-- # Highlight the last one
-- lines3d(t(yline), col="red", lwd=3)
--}
--
--par(opar)
--
--} # for (zzz in 0)
--rm(zzz)
Modified: trunk/packages/R/r-bioc-aroma.light/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-aroma.light/trunk/debian/rules 2017-05-12 18:42:13 UTC (rev 23739)
+++ trunk/packages/R/r-bioc-aroma.light/trunk/debian/rules 2017-05-15 10:45:57 UTC (rev 23740)
@@ -1,9 +1,16 @@
#!/usr/bin/make -f
-debRreposname=bioc
-include /usr/share/R/debian/r-cran.mk
+debRreposname := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}' | sed 's/r-\([a-z]\+\)-.*/\1/')
+awkString := "'/^(Package|Bundle):/ {print $$2 }'"
+cranNameOrig := $(shell awk "$(awkString)" DESCRIPTION)
+cranName := $(shell echo "$(cranNameOrig)" | tr A-Z a-z)
+package := r-$(debRreposname)-$(cranName)
-install/$(package)::
+%:
+ dh $@ --buildsystem R
+
+override_dh_install:
+ dh_install
mkdir -p debian/$(package)/usr/share/pixmaps/$(cranName)
for png in `find debian/$(package)/usr/lib/R/site-library/$(cranName) -name "*.png"` ; do \
mv $${png} debian/$(package)/usr/share/pixmaps/$(cranName) ; \
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