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 <[email protected]> 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 <[email protected]> -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 <[email protected]> +Copyright: 2006-2016 Henrik Bengtsson <[email protected]> License: GPL-2+ Files: debian/* -Copyright: 2015 Andreas Tille <[email protected]> +Copyright: 2015-2016 Andreas Tille <[email protected]> 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) ; \ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
