From 7bd1f97e8ee163490c8699917f4dab444eb1d0f5 Mon Sep 17 00:00:00 2001 From: Claus Wilke Date: Wed, 15 Nov 2017 23:17:44 -0600 Subject: [PATCH] preparing for CRAN submission, v 0.9.0 --- DESCRIPTION | 5 +- NAMESPACE | 1 + NEWS | 3 +- R/draw.R | 17 ++--- R/themes.R | 3 +- README.md | 2 +- cran-comments.md | 30 +++++--- man/draw_image.Rd | 14 ++-- man/draw_label.Rd | 22 +++--- man/draw_text.Rd | 15 ++-- man/theme_map.Rd | 26 +++++++ revdep/README.md | 147 ++++++++++++++++++++++++++++++------- revdep/checks.rds | Bin 0 -> 2695 bytes revdep/problems.md | 78 ++++++++++++++++---- revdep/timing.md | 34 +++++---- vignettes/introduction.Rmd | 3 +- 16 files changed, 295 insertions(+), 105 deletions(-) create mode 100644 man/theme_map.Rd create mode 100644 revdep/checks.rds diff --git a/DESCRIPTION b/DESCRIPTION index f14a427..8aa17f2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: cowplot Title: Streamlined Plot Theme and Plot Annotations for 'ggplot2' -Version: 0.8.0.9000 +Version: 0.9.0 Authors@R: c( person("Claus O.", "Wilke", role = c("aut", "cre"), email = "wilke@austin.utexas.edu"), person("RStudio", role = c("cph"), comment = "Copyright for ggplot2 code copied to cowplot" )) Description: Some helpful extensions and modifications to the 'ggplot2' @@ -25,11 +25,10 @@ License: GPL-2 LazyData: true Suggests: covr, - ggjoy, - ggstance, gridGraphics, knitr, magick, + maps, dplyr, tidyr, testthat, diff --git a/NAMESPACE b/NAMESPACE index 36f5153..4fd90f7 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -28,6 +28,7 @@ export(plot_grid) export(plot_to_gtable) export(save_plot) export(theme_cowplot) +export(theme_map) export(theme_nothing) import(ggplot2) importFrom(ggplot2,GeomCustomAnn) diff --git a/NEWS b/NEWS index a1236b6..80be404 100644 --- a/NEWS +++ b/NEWS @@ -1,5 +1,6 @@ -cowplot 0.8.0.9000 +cowplot 0.9.0 ---------------------------------------------------------------- +- Added a theme for maps, `theme_map()`. Code provided by Spencer Fox, https://github.com/sjfox. - Added `axis_canvas()` function and related functions to make marginal plots and plot annotations simpler - Now export the `plot_to_gtable` function which converts most diff --git a/R/draw.R b/R/draw.R index 0dab6a5..795b3c3 100644 --- a/R/draw.R +++ b/R/draw.R @@ -7,7 +7,7 @@ #' Draw a line from connected points #' #' Provide a sequence of x values and accompanying y values to draw a line on a plot. -#' +#' #' This is a convenience function, providing a wrapper around ggplot2's \code{geom_path}. #' #' @param x Vector of x coordinates. @@ -37,9 +37,9 @@ draw_line <- function(x, y, ...){ #' By default, the x and y coordinates specify the center of the text box. Set \code{hjust = 0, vjust = 0} to specify #' the lower left corner, and other values of \code{hjust} and \code{vjust} for any other relative location you want to #' specify. -#' +#' #' For a full list of ... options, see \code{\link{geom_label}}. -#' +#' #' @param text A vector of Character (not expressions) specifying the string(s) to be written. #' @param x Vector of x coordinates. #' @param y Vector of y coordinates. @@ -62,7 +62,7 @@ draw_text <- function(text, x = 0.5, y = 0.5, size = 14, hjust = 0.5, vjust = 0. aes(x = x, y = y, label = text), size = (size / .pt), # scale font size to match size in theme definition inherit.aes = FALSE, - hjust = hjust, + hjust = hjust, vjust = vjust, ...) } @@ -96,16 +96,16 @@ draw_text <- function(text, x = 0.5, y = 0.5, size = 14, hjust = 0.5, vjust = 0. #' c <- cor.test(mtcars$mpg, mtcars$disp, method = 'sp') #' label <- substitute(paste("Spearman ", rho, " = ", estimate, ", P = ", pvalue), #' list(estimate = signif(c$estimate, 2), pvalue = signif(c$p.value, 2))) -#' +#' #' # Add label to plot, centered on {x,y} (in data coordinates) #' p + draw_label(label, x = 20, y = 400) #' # Add label to plot in data coordinates, flush-left at x, baseline at y. #' p + draw_label(label, x = 20, y = 400, hjust = 0, vjust = 0) #' -#' # Add label to plot. Data coordinates, drawing rightward +#' # Add label to plot. Data coordinates, drawing rightward #' # from x, with ascenders of text touching y. #' p + draw_label(label, x = 20, y = 400, hjust = 0, vjust = 1) -#' +#' #' # Add labels via ggdraw. Uses ggdraw coordinates. #' # ggdraw coordinates default to xlim = c(0, 1), ylim = c(0, 1). #' ggdraw(p) + draw_label("centered on 70% of x, 90% of y height", x = 0.7, y = 0.9) @@ -252,8 +252,7 @@ draw_figure_label <- function(label, position = c("top.left", "top", "top.right" #' # Manipulate images and draw in plot coordinates #' img <- magick::image_read("http://jeroen.github.io/images/tiger.svg") #' img <- magick::image_transparent(img, color = "white") -#' img2 <- magick::image_charcoal(img) -#' img2 <- magick::image_transparent(img2, color = "white") +#' img2 <- magick::image_negate(img) #' ggplot(data.frame(x = 1:3, y = 1:3), aes(x, y)) + #' geom_point(size = 3) + #' geom_abline(slope = 1, intercept = 0, linetype = 2, color = "blue") + diff --git a/R/themes.R b/R/themes.R index 0550ec1..d59bb26 100644 --- a/R/themes.R +++ b/R/themes.R @@ -164,7 +164,8 @@ theme_nothing <- function(base_size = 14, base_family = ""){ #' usa_data = map_data("usa") #' ggplot(usa_data, aes(long, lat, group=region)) + geom_polygon() + theme_map() #' ggplot(usa_data, aes(long, lat, fill = region)) + geom_polygon() + theme_map() -#' ggplot(usa_data, aes(long, lat, fill = region)) + facet_wrap(~region, scales = "free") + geom_polygon() + theme_map() +#' ggplot(usa_data, aes(long, lat, fill = region)) + facet_wrap(~region, scales = "free") + +#' geom_polygon() + theme_map() #' @export theme_map <- function(base_size = 14, base_family = ""){ # work based off of theme_void diff --git a/README.md b/README.md index f7713d9..1830b2e 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ cowplot – An add-on to the ggplot2 plotting package [![Build Status](https://travis-ci.org/wilkelab/cowplot.svg?branch=master)](https://travis-ci.org/wilkelab/cowplot) [![Coverage Status](https://img.shields.io/codecov/c/github/wilkelab/cowplot/master.svg)](https://codecov.io/github/wilkelab/cowplot?branch=master) [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/cowplot)](https://CRAN.R-project.org/package=cowplot) -[![CRAN\_Downloads\_Badge](http://cranlogs.r-pkg.org/badges/grand-total/cowplot?color=brightgreen)](http://cranlogs.r-pkg.org/downloads/total/last-month/cowplot) +[![CRAN\_Downloads\_Badge](http://cranlogs.r-pkg.org/badges/cowplot)](http://cranlogs.r-pkg.org/downloads/total/last-month/cowplot) The cowplot package is meant to provide a publication-ready theme for ggplot2, one that requires a minimum amount of fiddling with sizes of axis labels, plot backgrounds, etc. It meets my personal needs; you may or may not like my style. diff --git a/cran-comments.md b/cran-comments.md index 20a2cc1..6408d69 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,8 +1,8 @@ This is a major improvement that fixes numerous bugs and adds two substantial new features. ## Test environments -* R devel and R 3.4.1 on win-builder [ via devtools::build_win() ] -* local OS X install x86_64-apple-darwin15.6.0 (64-bit), R 3.4.1 +* R devel and R 3.4.2 on win-builder [ via devtools::build_win() ] +* local OS X install x86_64-apple-darwin15.6.0 (64-bit), R 3.4.2 ## R CMD check results There were no ERRORs or WARNINGs. @@ -16,25 +16,33 @@ Both spellings are correct. ## Downstream dependencies Seem fine, according to devtools::revdep_check(). -The two packages with errors failed at the installation stage, +The packages with errors failed at the installation stage, not because of cowplot. Full results available at https://github.com/wilkelab/cowplot/blob/master/revdep/README.md -13 packages +21 packages |package |version | errors| warnings| notes| |:------------|:-------|------:|--------:|-----:| +|bigstatsr |0.2.2 | 1| 0| 0| |deconvolveR |1.0-3 | 0| 0| 0| |DGCA |1.0.1 | 1| 0| 0| -|ggjoy |0.2.0 | 0| 0| 0| -|ggpubr |0.1.4 | 0| 0| 0| +|ggpubr |0.1.6 | 0| 0| 1| |IncucyteDRC |0.5.4 | 0| 0| 0| -|jtools |0.4.5 | 0| 0| 1| +|jtools |0.9.0 | 0| 0| 1| |JWileymisc |0.2.1 | 0| 0| 0| +|meme |0.0.7 | 0| 0| 0| +|memery |0.3.1 | 0| 0| 0| +|modcmfitr |0.1.0 | 0| 0| 0| |oddsratio |1.0.0 | 0| 0| 0| -|poppr |2.4.1 | 1| 0| 0| -|preText |0.6.0 | 0| 0| 0| -|sicegar |0.2 | 0| 0| 0| -|tadaatoolbox |0.13.0 | 0| 0| 1| +|pcr |1.0.1 | 0| 0| 0| +|poppr |2.5.0 | 1| 0| 0| +|preText |0.6.1 | 0| 0| 0| +|RNOmni |0.1.3 | 0| 0| 0| +|Seurat |2.1.0 | 1| 0| 1| +|sicegar |0.2.2 | 0| 0| 0| +|survivALL |0.9.1 | 1| 0| 0| +|tadaatoolbox |0.14.0 | 0| 0| 1| |valr |0.3.1 | 0| 0| 1| +|vanddraabe |1.0.0 | 0| 0| 0| diff --git a/man/draw_image.Rd b/man/draw_image.Rd index 66454af..3fcd1e6 100644 --- a/man/draw_image.Rd +++ b/man/draw_image.Rd @@ -35,7 +35,7 @@ Places an image somewhere onto the drawing canvas. By default, coordinates run f } \examples{ # Use image as plot background -p <- ggplot(iris, aes(x=Sepal.Length, fill=Species)) + geom_density(alpha = 0.7) +p <- ggplot(iris, aes(x = Sepal.Length, fill = Species)) + geom_density(alpha = 0.7) ggdraw() + draw_image("http://jeroen.github.io/images/tiger.svg") + draw_plot(p + theme(legend.box.background = element_rect(color = "white"))) @@ -43,16 +43,16 @@ ggdraw() + # Manipulate images and draw in plot coordinates img <- magick::image_read("http://jeroen.github.io/images/tiger.svg") img <- magick::image_transparent(img, color = "white") -img2 <- magick::image_charcoal(img) -img2 <- magick::image_transparent(img2, color = "white") -ggplot(data.frame(x=1:3, y=1:3), aes(x, y)) + +img2 <- magick::image_negate(img) +ggplot(data.frame(x = 1:3, y = 1:3), aes(x, y)) + geom_point(size = 3) + geom_abline(slope = 1, intercept = 0, linetype = 2, color = "blue") + - draw_image(img, x=1, y=1, scale = .9) + - draw_image(img2, x=2, y=2, scale = .9) + draw_image(img , x = 1, y = 1, scale = .9) + + draw_image(img2, x = 2, y = 2, scale = .9) # Make grid with plot and image -p <- ggplot(iris, aes(x=Sepal.Length, fill=Species)) + geom_density(alpha = 0.7) +p <- ggplot(iris, aes(x = Sepal.Length, fill = Species)) + + geom_density(alpha = 0.7) p2 <- ggdraw() + draw_image("http://jeroen.github.io/images/tiger.svg", scale = 0.9) plot_grid(p, p2, labels = "AUTO") } diff --git a/man/draw_label.Rd b/man/draw_label.Rd index 5072909..bf4ffa3 100644 --- a/man/draw_label.Rd +++ b/man/draw_label.Rd @@ -15,9 +15,9 @@ draw_label(label, x = 0.5, y = 0.5, hjust = 0.5, vjust = 0.5, \item{y}{The y location (origin) of the label.} -\item{hjust}{Horizontal justification. Default = .5 (centred on x). 0 = flush-left at x, 1 = flush-right.} +\item{hjust}{Horizontal justification. Default = 0.5 (centered on x). 0 = flush-left at x, 1 = flush-right.} -\item{vjust}{Vertical justification. Default = .5 (centred on y). 0 = baseline at y, 1= ascender at y.} +\item{vjust}{Vertical justification. Default = 0.5 (centered on y). 0 = baseline at y, 1 = ascender at y.} \item{fontfamily}{The font family} @@ -45,8 +45,8 @@ specify. } \examples{ # setup plot and a label (regression description) -p <- ggplot(mtcars, aes(mpg, disp)) + geom_line(colour = "blue") + background_grid(minor='none') -c <- cor.test(mtcars$mpg, mtcars$disp, method='sp') +p <- ggplot(mtcars, aes(mpg, disp)) + geom_line(color = "blue") + background_grid(minor = 'none') +c <- cor.test(mtcars$mpg, mtcars$disp, method = 'sp') label <- substitute(paste("Spearman ", rho, " = ", estimate, ", P = ", pvalue), list(estimate = signif(c$estimate, 2), pvalue = signif(c$p.value, 2))) @@ -55,18 +55,18 @@ p + draw_label(label, x = 20, y = 400) # Add label to plot in data coordinates, flush-left at x, baseline at y. p + draw_label(label, x = 20, y = 400, hjust = 0, vjust = 0) -# Add label to plot. Data coordinates, drawing rightward +# Add label to plot. Data coordinates, drawing rightward # from x, with ascenders of text touching y. p + draw_label(label, x = 20, y = 400, hjust = 0, vjust = 1) - +# Add labels via ggdraw. Uses ggdraw coordinates. # ggdraw coordinates default to xlim = c(0, 1), ylim = c(0, 1). -ggdraw(p) + draw_label("Centred on 70\% of x, 90\% of y height", x = .7, y = .9) +ggdraw(p) + draw_label("centered on 70\% of x, 90\% of y height", x = 0.7, y = 0.9) labstr = "bottom left at {0\%, 0\%} of the SHEET, not the plot!" -p = ggdraw(p) + draw_label(labstr, x = 0, y = 0, hjust = 0, vjust=0) -p = p + draw_label("top right at {1,1}", x = 1, y = 1, hjust = 1, vjust=1) -p = p + draw_label("bottom left at {.4,.4}", x = .4, y = .4, hjust = 0, vjust=0) -p + draw_label("centred on at {.5,.5}", x = .5, y = .5, hjust = .5, vjust=.5) +p = ggdraw(p) + draw_label(labstr, x = 0, y = 0, hjust = 0, vjust = 0) +p = p + draw_label("top right at {1,1}", x = 1, y = 1, hjust = 1, vjust = 1) +p = p + draw_label("bottom left at {.4,.4}", x = 0.4, y = 0.4, hjust = 0, vjust = 0) +p + draw_label("centered on at {.5,.5}", x = 0.5, y = 0.5, hjust = 0.5, vjust = 0.5) } \seealso{ \code{\link{ggdraw}} diff --git a/man/draw_text.Rd b/man/draw_text.Rd index 565d1dd..0b58223 100644 --- a/man/draw_text.Rd +++ b/man/draw_text.Rd @@ -8,7 +8,7 @@ draw_text(text, x = 0.5, y = 0.5, size = 14, hjust = 0.5, vjust = 0.5, ...) } \arguments{ -\item{text}{A vector of strings (not (yet) expressions) specifying the text(s) to be written.} +\item{text}{A vector of Character (not expressions) specifying the string(s) to be written.} \item{x}{Vector of x coordinates.} @@ -16,9 +16,9 @@ draw_text(text, x = 0.5, y = 0.5, size = 14, hjust = 0.5, vjust = 0.5, \item{size}{Font size of the text to be drawn.} -\item{hjust}{(default = .5)} +\item{hjust}{(default = 0.5)} -\item{vjust}{(default = .5)} +\item{vjust}{(default = 0.5)} \item{...}{Style parameters, such as \code{colour}, \code{alpha}, \code{angle}, \code{size}, etc.} } @@ -37,8 +37,13 @@ specify. For a full list of ... options, see \code{\link{geom_label}}. } \examples{ -ggdraw() + draw_text(c("Hello World!", "to be or not to be", "over and out"), x = 1:3, y=1:3) -ggdraw() + draw_text("Hello World!", x = 1, y = 2) +# Draw onto a 1*1 drawing surface +ggdraw() + draw_text("Hello World!", x = 0.5, y = 0.5) +# +# Adorn a plot from the Anscombe data set of "identical" data. +p = qplot(x = x1, y = y1, geom = c("smooth", "point"), data = anscombe) +threeStrings = c("Hello World!", "to be or not to be", "over and out") +p + draw_text(threeStrings, x = 8:10, y = 5:7, hjust = 0) } \seealso{ \code{\link{draw_label}} diff --git a/man/theme_map.Rd b/man/theme_map.Rd new file mode 100644 index 0000000..ea41143 --- /dev/null +++ b/man/theme_map.Rd @@ -0,0 +1,26 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/themes.R +\name{theme_map} +\alias{theme_map} +\title{Create a theme for map plotting} +\usage{ +theme_map(base_size = 14, base_family = "") +} +\arguments{ +\item{base_size}{Overall font size. Default is 14.} + +\item{base_family}{Base font family.} +} +\value{ +The theme. +} +\description{ +The theme created by this function is useful for plotting maps with cowplot default sizing. +} +\examples{ +usa_data = map_data("usa") +ggplot(usa_data, aes(long, lat, group=region)) + geom_polygon() + theme_map() +ggplot(usa_data, aes(long, lat, fill = region)) + geom_polygon() + theme_map() +ggplot(usa_data, aes(long, lat, fill = region)) + facet_wrap(~region, scales = "free") + + geom_polygon() + theme_map() +} diff --git a/revdep/README.md b/revdep/README.md index 84818ef..884180c 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -4,39 +4,64 @@ |setting |value | |:--------|:----------------------------| -|version |R version 3.4.1 (2017-06-30) | +|version |R version 3.4.2 (2017-09-28) | |system |x86_64, darwin15.6.0 | |ui |RStudio (1.0.153) | |language |(EN) | |collate |en_US.UTF-8 | |tz |America/Chicago | -|date |2017-07-29 | +|date |2017-11-15 | ## Packages -|package |* |version |date |source | -|:-------|:--|:----------|:----------|:---------------------------| -|cowplot | |0.7.0.9990 |2017-07-30 |local (wilkelab/cowplot@NA) | +|package |* |version |date |source | +|:-------|:--|:-------|:----------|:---------------------------| +|covr | |3.0.1 |2017-11-07 |cran (@3.0.1) | +|cowplot | |0.9.0 |2017-11-15 |local (wilkelab/cowplot@NA) | +|dplyr |* |0.7.4 |2017-09-28 |cran (@0.7.4) | +|magick | |1.5 |2017-11-03 |cran (@1.5) | +|tidyr |* |0.7.2 |2017-10-16 |cran (@0.7.2) | +|vdiffr | |0.2.1 |2017-10-09 |cran (@0.2.1) | # Check results -13 packages +21 packages |package |version | errors| warnings| notes| |:------------|:-------|------:|--------:|-----:| +|bigstatsr |0.2.2 | 1| 0| 0| |deconvolveR |1.0-3 | 0| 0| 0| |DGCA |1.0.1 | 1| 0| 0| -|ggjoy |0.2.0 | 0| 0| 0| -|ggpubr |0.1.4 | 0| 0| 0| +|ggpubr |0.1.6 | 0| 0| 1| |IncucyteDRC |0.5.4 | 0| 0| 0| -|jtools |0.4.5 | 0| 0| 1| +|jtools |0.9.0 | 0| 0| 1| |JWileymisc |0.2.1 | 0| 0| 0| +|meme |0.0.7 | 0| 0| 0| +|memery |0.3.1 | 0| 0| 0| +|modcmfitr |0.1.0 | 0| 0| 0| |oddsratio |1.0.0 | 0| 0| 0| -|poppr |2.4.1 | 1| 0| 0| -|preText |0.6.0 | 0| 0| 0| -|sicegar |0.2 | 0| 0| 0| -|tadaatoolbox |0.13.0 | 0| 0| 1| +|pcr |1.0.1 | 0| 0| 0| +|poppr |2.5.0 | 1| 0| 0| +|preText |0.6.1 | 0| 0| 0| +|RNOmni |0.1.3 | 0| 0| 0| +|Seurat |2.1.0 | 1| 0| 1| +|sicegar |0.2.2 | 0| 0| 0| +|survivALL |0.9.1 | 1| 0| 0| +|tadaatoolbox |0.14.0 | 0| 0| 1| |valr |0.3.1 | 0| 0| 1| +|vanddraabe |1.0.0 | 0| 0| 0| + +## bigstatsr (0.2.2) +Maintainer: Florian Privé +Bug reports: https://github.com/privefl/bigstatsr/issues + +1 error | 0 warnings | 0 notes + +``` +checking whether package ‘bigstatsr’ can be installed ... ERROR +Installation failed. +See ‘/Users/wilke/github/cowplot/revdep/checks/bigstatsr.Rcheck/00install.out’ for details. +``` ## deconvolveR (1.0-3) Maintainer: Balasubramanian Narasimhan @@ -54,23 +79,23 @@ checking package dependencies ... ERROR Packages required but not available: ‘WGCNA’ ‘matrixStats’ Packages suggested but not available for checking: - ‘impute’ ‘gplots’ ‘fdrtool’ ‘GOstats’ ‘HGNChelper’ ‘org.Hs.eg.db’ - ‘AnnotationDbi’ ‘abind’ ‘MEGENA’ ‘doMC’ + ‘impute’ ‘fdrtool’ ‘GOstats’ ‘HGNChelper’ ‘org.Hs.eg.db’ + ‘AnnotationDbi’ ‘MEGENA’ ‘doMC’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ``` -## ggjoy (0.2.0) -Maintainer: Claus O. Wilke - -0 errors | 0 warnings | 0 notes - -## ggpubr (0.1.4) +## ggpubr (0.1.6) Maintainer: Alboukadel Kassambara Bug reports: https://github.com/kassambara/ggpubr/issues -0 errors | 0 warnings | 0 notes +0 errors | 0 warnings | 1 note + +``` +checking Rd cross-references ... NOTE +Package unavailable to check Rd xrefs: ‘FactoMineR’ +``` ## IncucyteDRC (0.5.4) Maintainer: Phil Chapman @@ -78,7 +103,7 @@ Bug reports: https://github.com/chapmandu2/IncucyteDRC/issues 0 errors | 0 warnings | 0 notes -## jtools (0.4.5) +## jtools (0.9.0) Maintainer: Jacob A. Long Bug reports: https://github.com/jacob-long/jtools/issues @@ -86,7 +111,7 @@ Bug reports: https://github.com/jacob-long/jtools/issues ``` checking Rd cross-references ... NOTE -Packages unavailable to check Rd xrefs: ‘arm’, ‘effects’, ‘rockchalk’, ‘pequod’ +Packages unavailable to check Rd xrefs: ‘effects’, ‘ReporteRs’, ‘arm’, ‘rockchalk’, ‘pequod’, ‘MuMIn’ ``` ## JWileymisc (0.2.1) @@ -95,13 +120,36 @@ Bug reports: https://github.com/JWiley/JWileymisc/issues 0 errors | 0 warnings | 0 notes +## meme (0.0.7) +Maintainer: Guangchuang Yu +Bug reports: https://github.com/GuangchuangYu/meme/issues + +0 errors | 0 warnings | 0 notes + +## memery (0.3.1) +Maintainer: Matthew Leonawicz +Bug reports: https://github.com/leonawicz/memery/issues + +0 errors | 0 warnings | 0 notes + +## modcmfitr (0.1.0) +Maintainer: Ed Wilson + +0 errors | 0 warnings | 0 notes + ## oddsratio (1.0.0) Maintainer: Patrick Schratz Bug reports: https://github.com/pat-s/oddsratio/issues 0 errors | 0 warnings | 0 notes -## poppr (2.4.1) +## pcr (1.0.1) +Maintainer: Mahmoud Ahmed +Bug reports: https://github.com/MahShaaban/pcr/issues + +0 errors | 0 warnings | 0 notes + +## poppr (2.5.0) Maintainer: Zhian N. Kamvar Bug reports: https://github.com/grunwaldlab/poppr/issues @@ -113,18 +161,55 @@ Installation failed. See ‘/Users/wilke/github/cowplot/revdep/checks/poppr.Rcheck/00install.out’ for details. ``` -## preText (0.6.0) +## preText (0.6.1) Maintainer: Matthew J. Denny 0 errors | 0 warnings | 0 notes -## sicegar (0.2) +## RNOmni (0.1.3) +Maintainer: Zachary McCaw + +0 errors | 0 warnings | 0 notes + +## Seurat (2.1.0) +Maintainer: Paul Hoffman +Bug reports: https://github.com/satijalab/seurat/issues + +1 error | 0 warnings | 1 note + +``` +checking whether package ‘Seurat’ can be installed ... ERROR +Installation failed. +See ‘/Users/wilke/github/cowplot/revdep/checks/Seurat.Rcheck/00install.out’ for details. + +checking package dependencies ... NOTE +Packages suggested but not available for checking: + ‘SummarizedExperiment’ ‘MAST’ ‘DESeq2’ +``` + +## sicegar (0.2.2) Maintainer: M. Umut Caglar Bug reports: https://github.com/wilkelab/sicegar/issues 0 errors | 0 warnings | 0 notes -## tadaatoolbox (0.13.0) +## survivALL (0.9.1) +Maintainer: Dominic Pearce + +1 error | 0 warnings | 0 notes + +``` +checking package dependencies ... ERROR +Packages required but not available: + ‘survcomp’ ‘survsim’ ‘Biobase’ ‘desiR’ ‘ggthemes’ ‘pander’ + +Package suggested but not available for checking: ‘GGally’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +``` + +## tadaatoolbox (0.14.0) Maintainer: Lukas Burk Bug reports: https://github.com/tadaadata/tadaatoolbox/issues @@ -147,3 +232,9 @@ Packages suggested but not available for checking: ‘GenomicRanges’ ‘IRanges’ ‘S4Vectors’ ``` +## vanddraabe (1.0.0) +Maintainer: Emilio Xavier Esposito +Bug reports: https://github.com/exeResearch/vanddraabe/issues + +0 errors | 0 warnings | 0 notes + diff --git a/revdep/checks.rds b/revdep/checks.rds new file mode 100644 index 0000000000000000000000000000000000000000..b65f78717aa9e9954e042a8c6108cb2c01a4e4ea GIT binary patch literal 2695 zcmV;23V8J&iwFP!000001La%GZ`;TjSNv?8O&{3qp=b{ir06;ij~-6qBrpm&w&FM& zJ6_4|W)~=o5ji3mksM}*l&qZm2edtRd+n(}4@GT89iGml}dA^`GvXC+`J6F4?hd=eN`&W%kVOMzYpIFAiW6B zpEOaAa$zwSt>as`hE{8p>c(2--dgSMwOrmGp5DE4a_81fq!Zq^-0E$72Ul`=e$Z_B zfo?IhTE!Jyy}h2VWMQ>&ke6Me?#XcrA0ItjyPHe;-j+kTrIGTs3BLx*C9j0Ntyb5n zx1s8}Ov<8594b`yWhGozx~k}s7zm#_DmE8bD)b$jxJEz>8W+=;Z4*C^&iOB6WppXc zHLTf0h+ID}dr-c^xN~B;9hRAoMU`o;KU}Z05%m>z+M`)0P}!SXwtu@-010 z>giUe!*dmva?cCb#|wr_F0RX&j3X6%4<CTR$wO}S z{`Lp7*@@!VgE+;tYTa;%Wn+ywKhIgk4b%5Malc$PEZ+>;GD|ru)v?QM%Md>C1ut7d z1T=3@7nAf{LI}4S1imYU^^b3U0iS=UzR&0S{#VVUTGw(7)HkVbQjXMkpfAsUo3!xd z+2=?D1=|!^E{JTK>Ih?u8qMa@=E`0qBfccj4ya0Xywaj!9pz&IQ&F@R_3&) zQ?DF$L8SWPW+*9FDylKe0$+9k=mY80hXw>zdX&=V5U}QBlu*tY7cs5%33ox+IKJpI zUk>aLgcdyFo4GN4_>I&EpV($b4uc6dh8a#c6@l%G2ysK&B%}d2azTHW##DEy9T-s1 zW84?Twv;oWm8dP>a*_;5yM>*5KT_``+s9H$-%Gjdw;m8+|DX-FLtJST2ZR%0IVJ=* zT^X*+;lVARfW2`YH+GH-tzy_H+F{YMPBrHCnBAkzVyn26$&t4U@W*TGiCvuhy(2$4 zyC{u5zag#`@&o#4ax7((nN2iZ-EwtK`)FVLh`KK=iZ+R(bs;!RsjqUy7It>Gw+f~| z^up2fm*P(mEnaXET8!xsI!#@jx|&5rhWZYb_duM!2rLe?*baOI(~n3GI!M|!y)S9- zlilruEy-aJc8Jfd)0QL&kgTM2h`@k{UsOrReQ~GmuOL~E<#>TlRiz!B`;6Htw)<45 z>SgTF?!mT6ZI5y#VBElu1f~Yo+p-H`bz3g97;^Yd+fo_#8@r99-#Xjh4m&KVT~IBg zdypTQ6zw!x+s(bhqrImGr~?i_7O`9e9wpSCTfQ93CTg7e)Rh1VRR@X)i2e4te8lFq zCbu~Wo!K{@L(;(^f-N~_&>N2DF*$s$mXr}x{p9W~tNaKTGJbrE#;3renr$O1F4lM@If=n8PP6cly z(AoZ6et!4vp)bm^u9gJnI{aX$>!9jXh>1ezgEx}MK( z`&@LGt~njcFMNZnBoNsB=Q%OQ6x+y&Dzk}#8;5d}3>Kv=&E&)f^6(-77Lj1Q+qqVB zrb7HRQD(X>xZL3ybE1-@=iwu_4paE-{cDm9i1UR{qRMQ-=l(u19TwcS6n>iR-%XmM~wmOGHH2vZ}Erqu#8LFFxzkT!A4o;GGHYaUXHV3azd#+gFP zyM|GHau|UUvk9Q9pPAv|6-FNsr$;#2eAx{H)4eVkJaGHO*5$dn$2@NgSQf*yys(CE zXISS)>qV>+Zvg!1P3O2_?eF9aH*D#A&TmIx{@`nOdzOHHC0?gL#%PDS?f}SAm(RMF zZhYkzTFV}%NA%RsBesI?WC-r#Gd02Qn&5V(nE6PN*_`{IenvEt@B!M_wn-l-&e1f| zuNxSIKy~`K>0fFdJat@aboQ$_JzszR$N&EKtVoa9ocy01lE6lfSf>-7pa>ekdQtUg zypt<>ITzqGo)hWfqDscRoVUWnJZNe|Z)VlPv%T2K{rOE!E~@^Wc)6&lujA%oO@8y$ z_X~zM?5DgM&b%SfFak9kMy@%M=H3}Xwet7^WK`zkLFAn;XX#k4$SB_ zF>JZY3?PEFFfyGHCf7HGrBQ>7S!gb+)VviAUm4t+=!Cs=u8vzNGMlhj-C>U9S{gc} zgliOS>QNkfVZ08kHhz;#1iWYUww^p01;M?{>TUT=?;97^-{u9Wh_htB0Lh*rCm9u% zqhb#%)+Qpp?4(m+HC5O!z!Nw$zU$->=mgK+tD2lU!<$pPz~qDf(Q8gqY!D?Vm`w}1 z@+9aIfgS|Bi#BZ;uD=L~3$xbd%*Q&N3!OHno zW)*aNreJbDH=MYm%Rg#F_XpoTNcScOX?DzJ6Q?&GlL2}}g`jqua^FOo&&dFrsbKsn z;ll#Na+kC%rm=F5*khIm3o@xR;u^9?XyocNH}HP_Ew6QVsSDmuYZBK;yujX2taa-b zK;r<{Zw1d&90$vxolP8<8;)gL3_T+~3*Orr!ehb$`q`wRyiQMPlM1B`KHI6E*U{h<_fb+^{_n9g)Wr|t6>R#?C)LC3pFR|eh5rCh zv!ZSltIXMpn<|64kf*wzxx1t)3ooOnyy}jD>PmXztOV&9Vk8L9fz}f literal 0 HcmV?d00001 diff --git a/revdep/problems.md b/revdep/problems.md index bb35bf0..bcc387a 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -4,28 +4,48 @@ |setting |value | |:--------|:----------------------------| -|version |R version 3.4.1 (2017-06-30) | +|version |R version 3.4.2 (2017-09-28) | |system |x86_64, darwin15.6.0 | |ui |RStudio (1.0.153) | |language |(EN) | |collate |en_US.UTF-8 | |tz |America/Chicago | -|date |2017-07-29 | +|date |2017-11-15 | ## Packages -|package |* |version |date |source | -|:-------|:--|:----------|:----------|:---------------------------| -|cowplot | |0.7.0.9990 |2017-07-30 |local (wilkelab/cowplot@NA) | +|package |* |version |date |source | +|:-------|:--|:-------|:----------|:---------------------------| +|covr | |3.0.1 |2017-11-07 |cran (@3.0.1) | +|cowplot | |0.9.0 |2017-11-15 |local (wilkelab/cowplot@NA) | +|dplyr |* |0.7.4 |2017-09-28 |cran (@0.7.4) | +|magick | |1.5 |2017-11-03 |cran (@1.5) | +|tidyr |* |0.7.2 |2017-10-16 |cran (@0.7.2) | +|vdiffr | |0.2.1 |2017-10-09 |cran (@0.2.1) | # Check results -2 packages with problems +5 packages with problems -|package |version | errors| warnings| notes| -|:-------|:-------|------:|--------:|-----:| -|DGCA |1.0.1 | 1| 0| 0| -|poppr |2.4.1 | 1| 0| 0| +|package |version | errors| warnings| notes| +|:---------|:-------|------:|--------:|-----:| +|bigstatsr |0.2.2 | 1| 0| 0| +|DGCA |1.0.1 | 1| 0| 0| +|poppr |2.5.0 | 1| 0| 0| +|Seurat |2.1.0 | 1| 0| 1| +|survivALL |0.9.1 | 1| 0| 0| + +## bigstatsr (0.2.2) +Maintainer: Florian Privé +Bug reports: https://github.com/privefl/bigstatsr/issues + +1 error | 0 warnings | 0 notes + +``` +checking whether package ‘bigstatsr’ can be installed ... ERROR +Installation failed. +See ‘/Users/wilke/github/cowplot/revdep/checks/bigstatsr.Rcheck/00install.out’ for details. +``` ## DGCA (1.0.1) Maintainer: Andrew McKenzie @@ -37,14 +57,14 @@ checking package dependencies ... ERROR Packages required but not available: ‘WGCNA’ ‘matrixStats’ Packages suggested but not available for checking: - ‘impute’ ‘gplots’ ‘fdrtool’ ‘GOstats’ ‘HGNChelper’ ‘org.Hs.eg.db’ - ‘AnnotationDbi’ ‘abind’ ‘MEGENA’ ‘doMC’ + ‘impute’ ‘fdrtool’ ‘GOstats’ ‘HGNChelper’ ‘org.Hs.eg.db’ + ‘AnnotationDbi’ ‘MEGENA’ ‘doMC’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ``` -## poppr (2.4.1) +## poppr (2.5.0) Maintainer: Zhian N. Kamvar Bug reports: https://github.com/grunwaldlab/poppr/issues @@ -56,3 +76,35 @@ Installation failed. See ‘/Users/wilke/github/cowplot/revdep/checks/poppr.Rcheck/00install.out’ for details. ``` +## Seurat (2.1.0) +Maintainer: Paul Hoffman +Bug reports: https://github.com/satijalab/seurat/issues + +1 error | 0 warnings | 1 note + +``` +checking whether package ‘Seurat’ can be installed ... ERROR +Installation failed. +See ‘/Users/wilke/github/cowplot/revdep/checks/Seurat.Rcheck/00install.out’ for details. + +checking package dependencies ... NOTE +Packages suggested but not available for checking: + ‘SummarizedExperiment’ ‘MAST’ ‘DESeq2’ +``` + +## survivALL (0.9.1) +Maintainer: Dominic Pearce + +1 error | 0 warnings | 0 notes + +``` +checking package dependencies ... ERROR +Packages required but not available: + ‘survcomp’ ‘survsim’ ‘Biobase’ ‘desiR’ ‘ggthemes’ ‘pander’ + +Package suggested but not available for checking: ‘GGally’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +``` + diff --git a/revdep/timing.md b/revdep/timing.md index 9d97d5c..5d80cd7 100644 --- a/revdep/timing.md +++ b/revdep/timing.md @@ -2,18 +2,26 @@ | |package |version | check_time| |:--|:------------|:-------|----------:| -|13 |valr |0.3.1 | 114.8| -|1 |deconvolveR |1.0-3 | 113.5| -|12 |tadaatoolbox |0.13.0 | 73.4| -|6 |jtools |0.4.5 | 72.1| -|4 |ggpubr |0.1.4 | 69.3| -|7 |JWileymisc |0.2.1 | 64| -|10 |preText |0.6.0 | 56.5| -|5 |IncucyteDRC |0.5.4 | 45| -|8 |oddsratio |1.0.0 | 44.3| -|11 |sicegar |0.2 | 42.1| -|3 |ggjoy |0.2.0 | 29.3| -|9 |poppr |2.4.1 | 3.9| -|2 |DGCA |1.0.1 | 2.1| +|15 |RNOmni |0.1.3 | 213.4| +|20 |valr |0.3.1 | 137.1| +|2 |deconvolveR |1.0-3 | 127.1| +|6 |jtools |0.9.0 | 99.2| +|19 |tadaatoolbox |0.14.0 | 86| +|4 |ggpubr |0.1.6 | 82.8| +|7 |JWileymisc |0.2.1 | 73.7| +|14 |preText |0.6.1 | 70| +|1 |bigstatsr |0.2.2 | 68.7| +|11 |oddsratio |1.0.0 | 51.9| +|17 |sicegar |0.2.2 | 51.4| +|5 |IncucyteDRC |0.5.4 | 48.1| +|10 |modcmfitr |0.1.0 | 47.7| +|12 |pcr |1.0.1 | 43| +|9 |memery |0.3.1 | 41.1| +|8 |meme |0.0.7 | 39.2| +|21 |vanddraabe |1.0.0 | 33.7| +|16 |Seurat |2.1.0 | 17.7| +|13 |poppr |2.5.0 | 6.3| +|18 |survivALL |0.9.1 | 2.9| +|3 |DGCA |1.0.1 | 2| diff --git a/vignettes/introduction.Rmd b/vignettes/introduction.Rmd index ed6e647..27a3f14 100644 --- a/vignettes/introduction.Rmd +++ b/vignettes/introduction.Rmd @@ -226,8 +226,7 @@ Or we can manipulate images and draw them in plot coordinates: ```{r message=FALSE, results="hide"} img <- magick::image_read("http://jeroen.github.io/images/tiger.svg") img <- magick::image_transparent(img, color = "white") -img2 <- magick::image_charcoal(img) -img2 <- magick::image_transparent(img2, color = "white") +img2 <- magick::image_negate(img) ``` ```{r message=FALSE}