diff --git a/.helper_functions b/.helper_functions index dbd74e7b6..b4ea70566 100644 --- a/.helper_functions +++ b/.helper_functions @@ -50,7 +50,8 @@ reverse_depends: do_check <- function() { devtools::revdep_check( bioconductor = TRUE, - ignore = c("nzelect"), + # ignore = c("nzelect"), + ignore = c(), libpath = .libPaths()[1], srcpath = normalizePath(file.path("revdep", "lib")) ) diff --git a/DESCRIPTION b/DESCRIPTION index f3d8bb3d5..2465f6381 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: GGally -Version: 1.3.1 +Version: 1.3.2 License: GPL (>= 2.0) Title: Extension to 'ggplot2' Type: Package @@ -29,6 +29,7 @@ Depends: R (>= 3.1) Imports: ggplot2 (>= 2.2.0), + grDevices, grid, gtable (>= 0.2.0), plyr (>= 1.8.3), diff --git a/NEWS.md b/NEWS.md index b1fd6f852..9137e410e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,20 @@ +GGally 1.3.2 +----------------- + +`ggpairs` and `ggduo` + +* Removed warning where pure numeric names gave a warning (#238, @lepennec) +* Fixed ordering issue with horizontal boxplots (#239) + +`ggparcoord` + +* Fixed missing `x` aes requirement when shadebox is provided (#237, @treysp) + +Package + +* Made igraph a non required dependency for tests (#240) + + GGally 1.3.1 ----------------- diff --git a/R/gg-plots.R b/R/gg-plots.R index d40607026..a6f060c32 100644 --- a/R/gg-plots.R +++ b/R/gg-plots.R @@ -577,7 +577,7 @@ ggally_dot_and_box_no_facet <- function(data, mapping, ..., boxPlot = TRUE) { if (horizontal) { p <- p + scale_x_discrete( - breaks = rev(levels(eval_data_col(data, mapping$x))) + limits = rev(levels(eval_data_col(data, mapping$x))) ) + coord_flip() } @@ -844,7 +844,7 @@ ggally_barDiag <- function(data, mapping, ..., rescale = FALSE){ } -#' GGplot Text +#' Text Plot #' #' Plot text for a plot. #' diff --git a/R/ggnetworkmap.R b/R/ggnetworkmap.R index e74846703..0cc6f47a9 100644 --- a/R/ggnetworkmap.R +++ b/R/ggnetworkmap.R @@ -39,7 +39,7 @@ if(getRversion() >= "2.15.1") { #' @param label.size size of the labels. Defaults to \code{size / 2}. #' @param ... other arguments supplied to geom_text for the node labels. Arguments pertaining to the title or other items can be achieved through ggplot2 methods. #' @author Amos Elberg \email{amos.elberg@@gmail.com}. Original by Moritz Marbach \email{mmarbach@@mail.uni-mannheim.de}, Francois Briatte \email{f.briatte@@gmail.com} -#' @details This is a function for plotting graphs generated by \code{network} or \code{igraph} in a more flexible and elegant manner than permitted by ggnet. The function does not need to be the first plot in the ggplot chain, so the graph can be plotted on top of a map or other chart. Segments can be straight lines, or plotted as great circles. Note that the great circles feature can produce odd results with arrows and with vertices beyond the plot edges; this is a gglot2 limitation and cannot yet be fixed. Nodes can have two color schemes, which are then plotted as the center and ring around the node. The color schemes are selected by adding scale_fill_ or scale_color_ just like any other ggplot2 plot. If there are no rings, scale_color sets the color of the nodes. If there are rings, scale_color sets the color of the rings, and scale_fill sets the color of the centers. Note that additional arguments in the ... are passed to geom_text for plotting labels. +#' @details This is a function for plotting graphs generated by \code{network} or \code{igraph} in a more flexible and elegant manner than permitted by ggnet. The function does not need to be the first plot in the ggplot chain, so the graph can be plotted on top of a map or other chart. Segments can be straight lines, or plotted as great circles. Note that the great circles feature can produce odd results with arrows and with vertices beyond the plot edges; this is a ggplot2 limitation and cannot yet be fixed. Nodes can have two color schemes, which are then plotted as the center and ring around the node. The color schemes are selected by adding scale_fill_ or scale_color_ just like any other ggplot2 plot. If there are no rings, scale_color sets the color of the nodes. If there are rings, scale_color sets the color of the rings, and scale_fill sets the color of the centers. Note that additional arguments in the ... are passed to geom_text for plotting labels. #' @importFrom utils installed.packages #' @examples #' # small function to display plots only if it's interactive diff --git a/R/ggpairs.R b/R/ggpairs.R index 8a87aac37..d95e10a55 100644 --- a/R/ggpairs.R +++ b/R/ggpairs.R @@ -127,18 +127,6 @@ fix_column_values <- function( } } - colnamesUsed <- colnamesData[columns] - nameIsOnlyNumber <- ! str_detect(colnamesUsed, "[^0-9]") - if (any(nameIsOnlyNumber)) { - badColumns <- colnamesUsed[nameIsOnlyNumber] - names(badColumns) <- paste("column =", columns[nameIsOnlyNumber]) - warning(paste( - "Data column name is numeric. Desired behavior may not be as expected.\n\n", - "c(", paste("'", names(badColumns), "' = '", badColumns, "'", collapse = "", sep = ""), ")", - sep = "" - )) - } - columns } @@ -518,7 +506,7 @@ ggduo <- function( sectionAes <- add_and_overwrite_aes( add_and_overwrite_aes( - aes_string(x = xColName, y = yColName), + aes_(x = as.name(xColName), y = as.name(yColName)), mapping ), types$mapping @@ -819,7 +807,7 @@ ggpairs <- function( sectionAes <- add_and_overwrite_aes( add_and_overwrite_aes( - aes_string(x = xColName, y = yColName), + aes_(x = as.name(xColName), y = as.name(yColName)), mapping ), types$mapping @@ -867,7 +855,7 @@ ggpairs <- function( #' #' @keywords internal #' @author Barret Schloerke \email{schloerke@@gmail.com} -#' @return aes_string output +#' @return aes_ output #' @import ggplot2 #' @rdname add_and_overwrite_aes #' @examples diff --git a/R/ggparcoord.R b/R/ggparcoord.R index 28da087b6..a1c7bb03b 100644 --- a/R/ggparcoord.R +++ b/R/ggparcoord.R @@ -249,6 +249,17 @@ ggparcoord <- function( stop("invalid value for 'boxplot'; must be a logical operator") } + if (!is.null(shadeBox) && length(shadeBox) != 1) { + stop("invalid value for 'shadeBox'; must be a single color") + } else { + valid_color <- tryCatch(is.matrix(grDevices::col2rgb(shadeBox)), + error = function(e) FALSE) + + if (!valid_color) { + stop("invalid value for 'shadeBox'; must be a valid R color") + } + } + if (is.logical(splineFactor)) { if (splineFactor) { splineFactor <- 3 @@ -498,6 +509,7 @@ ggparcoord <- function( data = d.sum, size = I(10), col = shadeBox, inherit.aes = FALSE, mapping = aes_string( + x = "variable", ymin = "min", ymax = "max", group = "variable" diff --git a/cran-comments.md b/cran-comments.md index 6d8ccc292..8bb544edf 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,82 +1,75 @@ ## Comments -### 2017-6-7 +### 2017-8-2 -vortexR has been updated to handle the new version of GGally. From my reverse dependency checks, there were no other affected packages. +No revdep authors were emailed as it is only small bug fixes or 'Suggest' dependency change for Brian. + +Please let me know if there is anything I can do. Thank you for your time. Best, Barret -### 2017-6-7 - -On CRAN -- @carlopacioni vortexR maintainer - - -### 2017-6-4 - -vortexR maintainer contacted. - +### 2017-7-18 -### 2017-6-4 +As §1.1.3.1 of the manual told you, packages in Suggests: should be used +conditionally. The latest version of igraph will not install on Solaris +(hence packages strictly depending on it), and as you can see from its +CRAN checks page, your package now fails its check. -~ Please give two weeks notice to affected packages. -- Uwe +Please correct ASAP and definitely within a month. +-- +Brian D. Ripley, -### 2017-6-2 - -No revdep authors were emailed as it is only small bug fixes, url link fixes, and new functions. - -Please let me know if there is anything I can do. Thank you for your time. - -Best, -Barret #### Test environments and R CMD check results * local OS X install - * R version 3.4.0 (2017-04-21) + * R version 3.4.1 (2017-06-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) - Running under: macOS Sierra 10.12.4 + Running under: macOS Sierra 10.12.5 * 0 errors | 0 warnings | 0 notes * travis-ci - * R version 3.4.0 (2017-04-21) + * R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu precise (12.04.5 LTS) * 0 errors | 0 warnings | 0 notes - * R Under development (unstable) (2017-05-24 r72734) + * R Under development (unstable) (2017-08-01 r73010) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu precise (12.04.5 LTS) * 0 errors | 0 warnings | 0 notes * win-builder (devel and release) - * R version 3.4.0 (2017-04-21) + * R version 3.4.1 (2017-06-30) * 0 errors | 0 warnings | 0 notes - * R Under development (unstable) (2017-06-01 r72753) + * R Under development (unstable) (2017-07-31 r73003) * 0 errors | 0 warnings | 0 notes ## Reverse dependencies Checked on - * R version 3.4.0 (2017-04-21) + * R version 3.4.1 (2017-06-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) - Running under: macOS Sierra 10.12.4 + Running under: macOS Sierra 10.12.5 No difference in test results due to GGally upgrade: Errors not related to GGally upgrade: -* Failed to install dependencies for: MissingDataGUI, specmine -* ggbio: checking examples ... ERROR -* POUMM: checking re-building of vignette outputs ... WARNING -* TVTB: checking tests ... ERROR -* Check failed to finish in 20 minutes, so ignored - * nzelect +|package |version | errors| warnings| notes| +|:--------------|:-------|------:|--------:|-----:| +|eechidna |1.1 | 0| 1| 1| - vignette building +|nzelect |0.3.3 | 0| 1| 0| - vignette building +|PopGenReport |3.0.0 | 0| 1| 1| - due to missing package dependencies +|POUMM |1.3.2 | 1| 0| 0| - can not install source package +|MissingDataGUI |0.2-5 | 1| 0| 0| - can not install dependencies +|specmine |1.0 | 1| 0| 0| - can not install dependencies + +* Side note, package 'Pi' took over 4 hours to check. diff --git a/man/add_and_overwrite_aes.Rd b/man/add_and_overwrite_aes.Rd index d340fc9e8..7df3295b5 100644 --- a/man/add_and_overwrite_aes.Rd +++ b/man/add_and_overwrite_aes.Rd @@ -7,7 +7,7 @@ add_and_overwrite_aes(current, new) } \value{ -aes_string output +aes_ output } \description{ Add new aesthetics to a previous aes. diff --git a/man/ggally_text.Rd b/man/ggally_text.Rd index a48cb2ee9..9be3eb016 100644 --- a/man/ggally_text.Rd +++ b/man/ggally_text.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/gg-plots.R \name{ggally_text} \alias{ggally_text} -\title{GGplot Text} +\title{Text Plot} \usage{ ggally_text(label, mapping = ggplot2::aes(color = "black"), xP = 0.5, yP = 0.5, xrange = c(0, 1), yrange = c(0, 1), ...) diff --git a/man/ggnetworkmap.Rd b/man/ggnetworkmap.Rd index 25e143ed3..e1f4e11ef 100644 --- a/man/ggnetworkmap.Rd +++ b/man/ggnetworkmap.Rd @@ -58,7 +58,7 @@ such as output from \code{ggmap}, \code{ggnetworkmap} will plot on top of that c Otherwise, \code{ggnetworkmap} will generate coordinates using the Fruchterman-Reingold algorithm. } \details{ -This is a function for plotting graphs generated by \code{network} or \code{igraph} in a more flexible and elegant manner than permitted by ggnet. The function does not need to be the first plot in the ggplot chain, so the graph can be plotted on top of a map or other chart. Segments can be straight lines, or plotted as great circles. Note that the great circles feature can produce odd results with arrows and with vertices beyond the plot edges; this is a gglot2 limitation and cannot yet be fixed. Nodes can have two color schemes, which are then plotted as the center and ring around the node. The color schemes are selected by adding scale_fill_ or scale_color_ just like any other ggplot2 plot. If there are no rings, scale_color sets the color of the nodes. If there are rings, scale_color sets the color of the rings, and scale_fill sets the color of the centers. Note that additional arguments in the ... are passed to geom_text for plotting labels. +This is a function for plotting graphs generated by \code{network} or \code{igraph} in a more flexible and elegant manner than permitted by ggnet. The function does not need to be the first plot in the ggplot chain, so the graph can be plotted on top of a map or other chart. Segments can be straight lines, or plotted as great circles. Note that the great circles feature can produce odd results with arrows and with vertices beyond the plot edges; this is a ggplot2 limitation and cannot yet be fixed. Nodes can have two color schemes, which are then plotted as the center and ring around the node. The color schemes are selected by adding scale_fill_ or scale_color_ just like any other ggplot2 plot. If there are no rings, scale_color sets the color of the nodes. If there are rings, scale_color sets the color of the rings, and scale_fill sets the color of the centers. Note that additional arguments in the ... are passed to geom_text for plotting labels. } \examples{ # small function to display plots only if it's interactive diff --git a/revdep/README.md b/revdep/README.md index b87df82f0..f72be808b 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -4,88 +4,91 @@ |setting |value | |:--------|:----------------------------| -|version |R version 3.4.0 (2017-04-21) | +|version |R version 3.4.1 (2017-06-30) | |system |x86_64, darwin15.6.0 | |ui |X11 | |language |(EN) | |collate |en_US.UTF-8 | |tz |America/Indiana/Indianapolis | -|date |2017-06-07 | +|date |2017-08-02 | ## Packages -|package |* |version |date |source | -|:------------|:--|:-------|:----------|:-----------------------| -|broom | |0.4.2 |2017-02-13 |CRAN (R 3.4.0) | -|chemometrics | |1.4.2 |2017-03-17 |CRAN (R 3.4.0) | -|geosphere | |1.5-5 |2016-06-15 |CRAN (R 3.4.0) | -|GGally |* |1.3.1 |2017-06-07 |local (ggobi/ggally@NA) | -|ggplot2 | |2.2.1 |2016-12-30 |CRAN (R 3.4.0) | -|gtable | |0.2.0 |2016-02-26 |CRAN (R 3.4.0) | -|igraph | |1.0.1 |2015-06-26 |CRAN (R 3.4.0) | -|intergraph | |2.0-2 |2016-12-05 |CRAN (R 3.4.0) | -|mapproj | |1.2-4 |2015-08-03 |CRAN (R 3.4.0) | -|maps | |3.1.1 |2016-07-27 |CRAN (R 3.4.0) | -|network | |1.13.0 |2015-09-19 |CRAN (R 3.4.0) | -|packagedocs | |0.4.0 |2016-11-04 |CRAN (R 3.4.0) | -|plyr | |1.8.4 |2016-06-08 |CRAN (R 3.4.0) | -|progress | |1.1.2 |2016-12-14 |CRAN (R 3.4.0) | -|RColorBrewer | |1.1-2 |2014-12-07 |CRAN (R 3.4.0) | -|reshape | |0.8.6 |2016-10-21 |CRAN (R 3.4.0) | -|rmarkdown | |1.5 |2017-04-26 |CRAN (R 3.4.0) | -|roxygen2 | |6.0.1 |2017-02-06 |CRAN (R 3.4.0) | -|scagnostics | |0.2-4 |2012-11-05 |CRAN (R 3.4.0) | -|scales | |0.4.1 |2016-11-09 |CRAN (R 3.4.0) | -|sna | |2.4 |2016-08-08 |CRAN (R 3.4.0) | -|testthat | |1.0.2 |2016-04-23 |CRAN (R 3.4.0) | +|package |* |version |date |source | +|:------------|:--|:-------|:----------|:--------------| +|broom | |0.4.2 |2017-02-13 |CRAN (R 3.4.0) | +|chemometrics | |1.4.2 |2017-03-17 |CRAN (R 3.4.0) | +|geosphere | |1.5-5 |2016-06-15 |CRAN (R 3.4.0) | +|GGally |* |1.3.1 |2017-06-08 |CRAN (R 3.4.1) | +|ggplot2 | |2.2.1 |2016-12-30 |CRAN (R 3.4.0) | +|gtable | |0.2.0 |2016-02-26 |CRAN (R 3.4.0) | +|igraph | |1.1.2 |2017-07-21 |cran (@1.1.2) | +|intergraph | |2.0-2 |2016-12-05 |CRAN (R 3.4.0) | +|mapproj | |1.2-5 |2017-06-08 |CRAN (R 3.4.0) | +|maps | |3.2.0 |2017-06-08 |cran (@3.2.0) | +|network | |1.13.0 |2015-09-19 |CRAN (R 3.4.0) | +|packagedocs | |0.4.0 |2016-11-04 |CRAN (R 3.4.0) | +|plyr | |1.8.4 |2016-06-08 |CRAN (R 3.4.0) | +|progress | |1.1.2 |2016-12-14 |CRAN (R 3.4.0) | +|RColorBrewer | |1.1-2 |2014-12-07 |CRAN (R 3.4.0) | +|reshape | |0.8.6 |2016-10-21 |CRAN (R 3.4.0) | +|rmarkdown | |1.6 |2017-06-15 |CRAN (R 3.4.0) | +|roxygen2 | |6.0.1 |2017-02-06 |CRAN (R 3.4.0) | +|scagnostics | |0.2-4 |2012-11-05 |CRAN (R 3.4.0) | +|scales | |0.4.1 |2016-11-09 |CRAN (R 3.4.0) | +|sna | |2.4 |2016-08-08 |CRAN (R 3.4.0) | +|testthat | |1.0.2 |2016-04-23 |CRAN (R 3.4.0) | # Check results -41 packages - -|package |version | errors| warnings| notes| -|:-------------------|:-------|------:|--------:|-----:| -|BANFF |2.0 | 0| 0| 0| -|BAS |1.4.6 | 0| 0| 0| -|clustrd |1.2.0 | 0| 0| 0| -|DescribeDisplay |0.2.5 | 0| 0| 0| -|eechidna |1.1 | 0| 0| 1| -|freqparcoord |1.0.1 | 0| 0| 0| -|ggbio |1.24.0 | 1| 0| 5| -|ggCompNet |0.1.0 | 0| 0| 1| -|ggmcmc |1.1 | 0| 0| 0| -|gsynth |1.0.3 | 0| 0| 0| -|httk |1.5 | 0| 0| 1| -|ICtest |0.2 | 0| 0| 2| -|imageData |0.1-26 | 0| 0| 0| -|isomiRs |1.4.0 | 0| 0| 2| -|jmv |0.7.3.5 | 0| 0| 0| -|LANDD |1.1.0 | 0| 0| 2| -|MAST |1.2.1 | 0| 0| 2| -|mbgraphic |1.0.0 | 0| 0| 0| -|MCbiclust |1.0.1 | 0| 0| 2| -|MissingDataGUI |0.2-5 | 1| 0| 0| -|mlrMBO |1.1.0 | 0| 0| 0| -|ParamHelpers |1.10 | 0| 0| 1| -|Pi |1.4.0 | 0| 0| 1| -|plotly |4.7.0 | 0| 0| 0| -|PopGenReport |3.0.0 | 0| 0| 1| -|POUMM |1.2.2 | 0| 1| 0| -|qualvar |0.1.0 | 0| 0| 0| -|robCompositions |2.0.3 | 0| 0| 2| -|robustbase |0.92-7 | 0| 0| 1| -|rrr |1.0.0 | 0| 0| 0| -|rwty |1.0.1 | 0| 0| 0| -|SHELF |1.2.3 | 0| 0| 0| -|specmine |1.0 | 1| 0| 0| -|spup |0.1-0 | 0| 0| 0| -|svdvis |0.1 | 0| 0| 0| -|texmex |2.3 | 0| 0| 1| -|toaster |0.5.5 | 0| 0| 0| -|TVTB |1.2.0 | 1| 1| 1| -|userfriendlyscience |0.6-1 | 0| 0| 0| -|vdmR |0.2.3 | 0| 0| 0| -|vortexR |1.1.4 | 0| 0| 0| +44 packages + +|package |version | errors| warnings| notes| +|:---------------------|:-------|------:|--------:|-----:| +|BANFF |2.0 | 0| 0| 0| +|BAS |1.4.6 | 0| 0| 0| +|CINNA |1.0.0 | 0| 0| 0| +|clustrd |1.2.0 | 0| 0| 0| +|DescribeDisplay |0.2.5 | 0| 0| 0| +|eechidna |1.1 | 0| 1| 1| +|freqparcoord |1.0.1 | 0| 0| 0| +|ggbio |1.24.1 | 0| 0| 4| +|ggCompNet |0.1.0 | 0| 0| 1| +|ggmcmc |1.1 | 0| 0| 0| +|gsynth |1.0.3 | 0| 0| 0| +|httk |1.7 | 0| 0| 1| +|ICtest |0.3 | 0| 0| 1| +|imageData |0.1-26 | 0| 0| 0| +|isomiRs |1.4.0 | 0| 0| 2| +|jmv |0.7.3.5 | 0| 0| 0| +|LANDD |1.1.0 | 0| 0| 2| +|MAST |1.2.1 | 0| 0| 2| +|mbgraphic |1.0.0 | 0| 0| 0| +|MCbiclust |1.0.1 | 0| 0| 2| +|MissingDataGUI |0.2-5 | 1| 0| 0| +|mlrMBO |1.1.0 | 0| 0| 0| +|nzelect |0.3.3 | 0| 1| 0| +|ParamHelpers |1.10 | 0| 0| 1| +|Pi |1.4.0 | 0| 0| 1| +|plotly |4.7.1 | 0| 0| 0| +|PopGenReport |3.0.0 | 0| 1| 1| +|POUMM |1.3.2 | 1| 0| 0| +|qualvar |0.1.0 | 0| 0| 0| +|randomForestExplainer |0.9 | 0| 0| 0| +|robCompositions |2.0.5 | 0| 0| 1| +|robustbase |0.92-7 | 0| 0| 1| +|rrr |1.0.0 | 0| 0| 0| +|rwty |1.0.1 | 0| 0| 0| +|SHELF |1.2.3 | 0| 0| 0| +|specmine |1.0 | 1| 0| 0| +|spup |0.1-1 | 0| 0| 0| +|svdvis |0.1 | 0| 0| 0| +|texmex |2.3 | 0| 0| 1| +|toaster |0.5.5 | 0| 0| 0| +|TVTB |1.2.0 | 0| 0| 0| +|userfriendlyscience |0.6-1 | 0| 0| 0| +|vdmR |0.2.4 | 0| 0| 0| +|vortexR |1.1.4 | 0| 0| 0| ## BANFF (2.0) Maintainer: Tianwei Yu @@ -97,6 +100,11 @@ Maintainer: Merlise Clyde 0 errors | 0 warnings | 0 notes +## CINNA (1.0.0) +Maintainer: Minoo Ashtiani + +0 errors | 0 warnings | 0 notes + ## clustrd (1.2.0) Maintainer: Angelos Markos @@ -111,9 +119,32 @@ Bug reports: https://github.com/ggobi/DescribeDisplay/issues ## eechidna (1.1) Maintainer: Ben Marwick -0 errors | 0 warnings | 1 note +0 errors | 1 warning | 1 note ``` +checking re-building of vignette outputs ... WARNING +Error in re-building vignettes: + ... + + nasa + +Warning: Removed 10 rows containing non-finite values (stat_smooth). +Warning: Removed 10 rows containing missing values (geom_point). + +Attaching package: 'readr' +... 8 lines ... + StateAb = col_character(), + GivenNm = col_character(), + Surname = col_character(), + PartyNm = col_character(), + PartyAb = col_character(), + ElectedOrder = col_integer() +) +Quitting from lines 154-171 (exploring-election-data2016.Rmd) +Error: processing vignette 'exploring-election-data2016.Rmd' failed with diagnostics: +Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'integer' +Execution halted + checking installed package size ... NOTE installed size is 6.3Mb sub-directories of 1Mb or more: @@ -126,40 +157,13 @@ Maintainer: Norm Matloff 0 errors | 0 warnings | 0 notes -## ggbio (1.24.0) +## ggbio (1.24.1) Maintainer: Michael Lawrence Bug reports: https://github.com/tengfei/ggbio/issues -1 error | 0 warnings | 5 notes - -``` -checking examples ... ERROR -Running examples in ‘ggbio-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: autoplot -> ### Title: Generic autoplot function -> ### Aliases: autoplot autoplot,GRanges-method autoplot,GRangesList-method -> ### autoplot,IRanges-method autoplot,Seqinfo-method -> ### autoplot,BSgenome-method autoplot,GAlignments-method -... 416 lines ... -reduce alignemnts... -> -> -> ################################################### -> ### EnsDb -> ################################################### -> ## Fetching gene models from an EnsDb object. -> library(EnsDb.Hsapiens.v75) -Error in library(EnsDb.Hsapiens.v75) : - there is no package called 'EnsDb.Hsapiens.v75' -Execution halted - -checking package dependencies ... NOTE -Packages suggested but not available for checking: - ‘BSgenome.Hsapiens.UCSC.hg19’ ‘EnsDb.Hsapiens.v75’ +0 errors | 0 warnings | 4 notes +``` checking top-level files ... NOTE Non-standard file/directory found at top level: ‘TODO.org’ @@ -234,36 +238,27 @@ Maintainer: Yiqing Xu 0 errors | 0 warnings | 0 notes -## httk (1.5) +## httk (1.7) Maintainer: John Wambaugh 0 errors | 0 warnings | 1 note ``` checking installed package size ... NOTE - installed size is 13.9Mb + installed size is 13.7Mb sub-directories of 1Mb or more: data 12.2Mb - doc 1.3Mb + doc 1.0Mb ``` -## ICtest (0.2) -Maintainer: Klaus Nordhausen +## ICtest (0.3) +Maintainer: Klaus Nordhausen -0 errors | 0 warnings | 2 notes +0 errors | 0 warnings | 1 note ``` checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘fICA’ - -checking compiled code ... NOTE -File ‘ICtest/libs/ICtest.so’: - Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’ - -It is good practice to register native routines and to disable symbol -search. - -See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ``` ## imageData (0.1-26) @@ -396,6 +391,22 @@ Bug reports: https://github.com/mlr-org/mlrMBO/issues 0 errors | 0 warnings | 0 notes +## nzelect (0.3.3) +Maintainer: Peter Ellis + +0 errors | 1 warning | 0 notes + +``` +checking re-building of vignette outputs ... WARNING +Error in re-building vignettes: + ... +Quitting from lines 208-225 (README.Rmd) +Error: processing vignette 'README.Rmd' failed with diagnostics: +Evaluation error: votes, parties, and electorates should all be vectors of the same length. +Execution halted + +``` + ## ParamHelpers (1.10) Maintainer: Bernd Bischl Bug reports: https://github.com/berndbischl/ParamHelpers/issues @@ -426,7 +437,7 @@ checking installed package size ... NOTE doc 5.2Mb ``` -## plotly (4.7.0) +## plotly (4.7.1) Maintainer: Carson Sievert Bug reports: https://github.com/ropensci/plotly/issues @@ -435,41 +446,27 @@ Bug reports: https://github.com/ropensci/plotly/issues ## PopGenReport (3.0.0) Maintainer: Bernd Gruber -0 errors | 0 warnings | 1 note +0 errors | 1 warning | 1 note ``` +checking whether package ‘PopGenReport’ can be installed ... WARNING +Found the following significant warnings: + Warning: namespace ‘DBI’ is not available and has been replaced +See ‘/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/checks/PopGenReport.Rcheck/00install.out’ for details. + checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘ecodist’ ``` -## POUMM (1.2.2) +## POUMM (1.3.2) Maintainer: Venelin Mitov -0 errors | 1 warning | 0 notes +1 error | 0 warnings | 0 notes ``` -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... - the condition has length > 1 and only the first element will be used -Warning in if (alpha == 0) { : - the condition has length > 1 and only the first element will be used -Warning in window.mcmc(mc$mcmc, start = start, end = end, thin = thinMCMC) : - end value not changed -Warning in if (alpha == 0) { : - the condition has length > 1 and only the first element will be used -... 8 lines ... - the condition has length > 1 and only the first element will be used -Warning in FUN(X[[i]], ...) : end value not changed -Warning in FUN(X[[i]], ...) : end value not changed -Warning in FUN(X[[i]], ...) : end value not changed -Warning in FUN(X[[i]], ...) : end value not changed -Warning in FUN(X[[i]], ...) : end value not changed -Warning in FUN(X[[i]], ...) : end value not changed -Quitting from lines 393-404 (UserGuide.Rmd) -Error: processing vignette 'UserGuide.Rmd' failed with diagnostics: -package 'adaptMCMC' not found -Execution halted +checking whether package ‘POUMM’ can be installed ... ERROR +Installation failed. +See ‘/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/checks/POUMM.Rcheck/00install.out’ for details. ``` ## qualvar (0.1.0) @@ -477,23 +474,19 @@ Maintainer: Joel Gombin 0 errors | 0 warnings | 0 notes -## robCompositions (2.0.3) -Maintainer: Matthias Templ - -0 errors | 0 warnings | 2 notes +## randomForestExplainer (0.9) +Maintainer: Aleksandra Paluszynska -``` -checking Rd cross-references ... NOTE -Package unavailable to check Rd xrefs: ‘StatDA’ +0 errors | 0 warnings | 0 notes -checking compiled code ... NOTE -File ‘robCompositions/libs/robCompositions.so’: - Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’ +## robCompositions (2.0.5) +Maintainer: Matthias Templ -It is good practice to register native routines and to disable symbol -search. +0 errors | 0 warnings | 1 note -See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. +``` +checking Rd cross-references ... NOTE +Packages unavailable to check Rd xrefs: ‘mvoutlier’, ‘StatDA’ ``` ## robustbase (0.92-7) @@ -535,8 +528,8 @@ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ``` -## spup (0.1-0) -Maintainer: Kasia Sawicka +## spup (0.1-1) +Maintainer: Kasia Sawicka 0 errors | 0 warnings | 0 notes @@ -571,60 +564,14 @@ Bug reports: https://github.com/teradata-aster-field/toaster/issues Maintainer: Kevin Rue-Albrecht Bug reports: https://github.com/kevinrue/TVTB/issues -1 error | 1 warning | 1 note - -``` -checking tests ... ERROR - Running ‘testthat.R’ [14s/15s] -Running the tests in ‘tests/testthat.R’ failed. -Last 13 lines of output: - rs1426654 rs150379789 rs570906312 rs538198029 rs553496066 rs574775672 - TRUE TRUE FALSE FALSE TRUE FALSE - rs140666229 rs556950130 rs575303689 rs147513140 rs187525777 rs192454382 - TRUE FALSE TRUE TRUE FALSE FALSE - rs184818838 rs566886499 rs199924625 rs555872528 rs531820822 rs201353600 - FALSE FALSE FALSE FALSE FALSE FALSE - rs550201688 rs565338261 rs201239799 rs200461129 rs146726548 - FALSE FALSE FALSE FALSE TRUE - testthat results ================================================================ - OK: 229 SKIPPED: 0 FAILED: 2 - 1. Error: all signatures work to completion (@test_plotInfo-methods.R#25) - 2. Error: invalid metric/phenotype combination is detected (@test_plotInfo-methods.R#50) - - Error: testthat unit tests failed - Execution halted - -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Overwriting INFO keys in data: -- REF -- HET -- ALT -- AAF -- MAF -Overwriting INFO keys in header: -- REF -- HET -- ALT -- AAF -- MAF -Quitting from lines 570-577 (Introduction.Rmd) -Error: processing vignette 'Introduction.Rmd' failed with diagnostics: -there is no package called 'EnsDb.Hsapiens.v75' -Execution halted - - -checking package dependencies ... NOTE -Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’ -``` +0 errors | 0 warnings | 0 notes ## userfriendlyscience (0.6-1) Maintainer: Gjalt-Jorn Peters 0 errors | 0 warnings | 0 notes -## vdmR (0.2.3) +## vdmR (0.2.4) Maintainer: Tomokazu Fujino 0 errors | 0 warnings | 0 notes diff --git a/revdep/install/BSgenome.Hsapiens.UCSC.hg19.out b/revdep/install/BSgenome.Hsapiens.UCSC.hg19.out deleted file mode 100644 index 38fb692ef..000000000 --- a/revdep/install/BSgenome.Hsapiens.UCSC.hg19.out +++ /dev/null @@ -1,9 +0,0 @@ -* installing *source* package ‘BSgenome.Hsapiens.UCSC.hg19’ ... -** R -** inst -** preparing package for lazy loading -Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): - there is no package called ‘GenomeInfoDbData’ -Error : package ‘GenomeInfoDb’ could not be loaded -ERROR: lazy loading failed for package ‘BSgenome.Hsapiens.UCSC.hg19’ -* removing ‘/Users/barret/R/BSgenome.Hsapiens.UCSC.hg19’ diff --git a/revdep/install/EnsDb.Hsapiens.v75.out b/revdep/install/EnsDb.Hsapiens.v75.out deleted file mode 100644 index 282aea48c..000000000 --- a/revdep/install/EnsDb.Hsapiens.v75.out +++ /dev/null @@ -1,9 +0,0 @@ -* installing *source* package ‘EnsDb.Hsapiens.v75’ ... -** R -** inst -** preparing package for lazy loading -Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): - there is no package called ‘GenomeInfoDbData’ -Error : package ‘GenomeInfoDb’ could not be loaded -ERROR: lazy loading failed for package ‘EnsDb.Hsapiens.v75’ -* removing ‘/Users/barret/R/EnsDb.Hsapiens.v75’ diff --git a/revdep/problem-diff.txt b/revdep/problem-diff.txt index 94a6d2c23..66ba09719 100644 --- a/revdep/problem-diff.txt +++ b/revdep/problem-diff.txt @@ -1,12 +1,35 @@ -18c18 -< |:------------|:--|:-------|:----------|:-----------------------| +65c65 +< nasa --- -> |:------------|:--|:-------|:----------|:--------------| -22c22 -< |GGally |* |1.3.1 |2017-06-07 |local (ggobi/ggally@NA) | +> intersect, setdiff, setequal, union +67,68d66 +< Warning: Removed 10 rows containing non-finite values (stat_smooth). +< Warning: Removed 10 rows containing missing values (geom_point). +70c68,70 +< Attaching package: 'readr' --- -> |GGally |* |1.3.0 |2016-11-13 |cran (@1.3.0) | -202c202 -< Running ‘testthat.R’ [14s/15s] +> Attaching package: 'purrr' +> +> The following objects are masked from 'package:dplyr': +72,81c72,81 +< StateAb = col_character(), +< GivenNm = col_character(), +< Surname = col_character(), +< PartyNm = col_character(), +< PartyAb = col_character(), +< ElectedOrder = col_integer() +< ) +< Quitting from lines 154-171 (exploring-election-data2016.Rmd) +< Error: processing vignette 'exploring-election-data2016.Rmd' failed with diagnostics: +< Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'integer' --- -> Running ‘testthat.R’ [15s/15s] +> +> Attaching package: 'scales' +> +> The following object is masked from 'package:purrr': +> +> discard +> +> Quitting from lines 155-172 (exploring-election-data.Rmd) +> Error: processing vignette 'exploring-election-data.Rmd' failed with diagnostics: +> Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'logical' diff --git a/revdep/problems-cran.md b/revdep/problems-cran.md index de15915fd..c0e5f70ab 100644 --- a/revdep/problems-cran.md +++ b/revdep/problems-cran.md @@ -4,13 +4,13 @@ |setting |value | |:--------|:----------------------------| -|version |R version 3.4.0 (2017-04-21) | +|version |R version 3.4.1 (2017-06-30) | |system |x86_64, darwin15.6.0 | |ui |X11 | |language |(EN) | |collate |en_US.UTF-8 | |tz |America/Indiana/Indianapolis | -|date |2017-06-07 | +|date |2017-08-02 | ## Packages @@ -19,20 +19,20 @@ |broom | |0.4.2 |2017-02-13 |CRAN (R 3.4.0) | |chemometrics | |1.4.2 |2017-03-17 |CRAN (R 3.4.0) | |geosphere | |1.5-5 |2016-06-15 |CRAN (R 3.4.0) | -|GGally |* |1.3.0 |2016-11-13 |cran (@1.3.0) | +|GGally |* |1.3.1 |2017-06-08 |CRAN (R 3.4.1) | |ggplot2 | |2.2.1 |2016-12-30 |CRAN (R 3.4.0) | |gtable | |0.2.0 |2016-02-26 |CRAN (R 3.4.0) | -|igraph | |1.0.1 |2015-06-26 |CRAN (R 3.4.0) | +|igraph | |1.1.2 |2017-07-21 |cran (@1.1.2) | |intergraph | |2.0-2 |2016-12-05 |CRAN (R 3.4.0) | -|mapproj | |1.2-4 |2015-08-03 |CRAN (R 3.4.0) | -|maps | |3.1.1 |2016-07-27 |CRAN (R 3.4.0) | +|mapproj | |1.2-5 |2017-06-08 |CRAN (R 3.4.0) | +|maps | |3.2.0 |2017-06-08 |cran (@3.2.0) | |network | |1.13.0 |2015-09-19 |CRAN (R 3.4.0) | |packagedocs | |0.4.0 |2016-11-04 |CRAN (R 3.4.0) | |plyr | |1.8.4 |2016-06-08 |CRAN (R 3.4.0) | |progress | |1.1.2 |2016-12-14 |CRAN (R 3.4.0) | |RColorBrewer | |1.1-2 |2014-12-07 |CRAN (R 3.4.0) | |reshape | |0.8.6 |2016-10-21 |CRAN (R 3.4.0) | -|rmarkdown | |1.5 |2017-04-26 |CRAN (R 3.4.0) | +|rmarkdown | |1.6 |2017-06-15 |CRAN (R 3.4.0) | |roxygen2 | |6.0.1 |2017-02-06 |CRAN (R 3.4.0) | |scagnostics | |0.2-4 |2012-11-05 |CRAN (R 3.4.0) | |scales | |0.4.1 |2016-11-09 |CRAN (R 3.4.0) | @@ -41,98 +41,51 @@ # Check results -5 packages with problems +6 packages with problems |package |version | errors| warnings| notes| |:--------------|:-------|------:|--------:|-----:| -|ggbio |1.24.0 | 1| 0| 5| +|eechidna |1.1 | 0| 1| 1| |MissingDataGUI |0.2-5 | 1| 0| 0| -|POUMM |1.2.2 | 0| 1| 0| +|nzelect |0.3.3 | 0| 1| 0| +|PopGenReport |3.0.0 | 0| 1| 1| +|POUMM |1.3.2 | 1| 0| 0| |specmine |1.0 | 1| 0| 0| -|TVTB |1.2.0 | 1| 1| 1| -## ggbio (1.24.0) -Maintainer: Michael Lawrence -Bug reports: https://github.com/tengfei/ggbio/issues +## eechidna (1.1) +Maintainer: Ben Marwick -1 error | 0 warnings | 5 notes +0 errors | 1 warning | 1 note ``` -checking examples ... ERROR -Running examples in ‘ggbio-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: autoplot -> ### Title: Generic autoplot function -> ### Aliases: autoplot autoplot,GRanges-method autoplot,GRangesList-method -> ### autoplot,IRanges-method autoplot,Seqinfo-method -> ### autoplot,BSgenome-method autoplot,GAlignments-method -... 416 lines ... -reduce alignemnts... -> -> -> ################################################### -> ### EnsDb -> ################################################### -> ## Fetching gene models from an EnsDb object. -> library(EnsDb.Hsapiens.v75) -Error in library(EnsDb.Hsapiens.v75) : - there is no package called 'EnsDb.Hsapiens.v75' +checking re-building of vignette outputs ... WARNING +Error in re-building vignettes: + ... + + intersect, setdiff, setequal, union + + +Attaching package: 'purrr' + +The following objects are masked from 'package:dplyr': +... 8 lines ... + +Attaching package: 'scales' + +The following object is masked from 'package:purrr': + + discard + +Quitting from lines 155-172 (exploring-election-data.Rmd) +Error: processing vignette 'exploring-election-data.Rmd' failed with diagnostics: +Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'logical' Execution halted -checking package dependencies ... NOTE -Packages suggested but not available for checking: - ‘BSgenome.Hsapiens.UCSC.hg19’ ‘EnsDb.Hsapiens.v75’ - -checking top-level files ... NOTE -Non-standard file/directory found at top level: - ‘TODO.org’ - -checking dependencies in R code ... NOTE -Unexported objects imported by ':::' calls: - 'S4Vectors:::top_prenv' 'ggplot2:::add_ggplot' 'ggplot2:::cunion' - 'ggplot2:::rename_aes' 'ggplot2:::rescale01' - 'ggplot2:::set_last_plot' - See the note in ?`:::` about the use of this operator. - -checking R code for possible problems ... NOTE -.combineNames: no visible binding for global variable - '.layout_circle.stats' -Ideogram: no visible global function definition for 'data' -Ideogram: no visible binding for global variable 'ideoCyto' -Ideogram: no visible binding for global variable 'cytobands' -ScalePlot: no visible binding for global variable 'y' -ScalePlot2: no visible binding for global variable 'breaks' -ScalePlot2: no visible binding for global variable 'yend' -ScalePlot2: no visible binding for global variable 'y.text' -... 48 lines ... - .fragLength .layout_circle.stats .x breaks coefs cytobands data eds - fe fl gieStain ideoCyto indexProbesProcessed midpoint mt name read se - stepping sts value variable x xend y y.text y2 yend yend2 -Consider adding - importFrom("utils", "data") -to your NAMESPACE file. - -Found the following calls to data() loading into the global environment: -File ‘ggbio/R/ideogram.R’: - data(ideoCyto, package = "biovizBase") -See section ‘Good practice’ in ‘?data’. - -checking Rd line widths ... NOTE -Rd file 'autoplot-method.Rd': - \usage lines wider than 90 characters: - autoplot(object, ..., type = c("heatmap", "link", "pcp", "boxplot", "scatterplot.matrix"), pheno.plot = FALSE, - -Rd file 'geom_arrowrect-method.Rd': - \examples lines wider than 100 characters: - ggplot(gr) + geom_arrowrect(gr, stat = "stepping", aes(y = value, group = pair), group.selfish = FALSE) - -Rd file 'plotSingleChrom.Rd': - \usage lines wider than 90 characters: - plotIdeogram(obj, subchr = NULL, zoom.region = NULL, which = NULL, xlab, ylab, main, xlabel = - -These lines will be truncated in the PDF manual. +checking installed package size ... NOTE + installed size is 6.3Mb + sub-directories of 1Mb or more: + data 4.9Mb + doc 1.2Mb ``` ## MissingDataGUI (0.2-5) @@ -148,8 +101,8 @@ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ``` -## POUMM (1.2.2) -Maintainer: Venelin Mitov +## nzelect (0.3.3) +Maintainer: Peter Ellis 0 errors | 1 warning | 0 notes @@ -157,88 +110,49 @@ Maintainer: Venelin Mitov checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... - the condition has length > 1 and only the first element will be used -Warning in if (alpha == 0) { : - the condition has length > 1 and only the first element will be used -Warning in window.mcmc(mc$mcmc, start = start, end = end, thin = thinMCMC) : - end value not changed -Warning in if (alpha == 0) { : - the condition has length > 1 and only the first element will be used -... 8 lines ... - the condition has length > 1 and only the first element will be used -Warning in FUN(X[[i]], ...) : end value not changed -Warning in FUN(X[[i]], ...) : end value not changed -Warning in FUN(X[[i]], ...) : end value not changed -Warning in FUN(X[[i]], ...) : end value not changed -Warning in FUN(X[[i]], ...) : end value not changed -Warning in FUN(X[[i]], ...) : end value not changed -Quitting from lines 393-404 (UserGuide.Rmd) -Error: processing vignette 'UserGuide.Rmd' failed with diagnostics: -package 'adaptMCMC' not found +Quitting from lines 208-225 (README.Rmd) +Error: processing vignette 'README.Rmd' failed with diagnostics: +Evaluation error: votes, parties, and electorates should all be vectors of the same length. Execution halted + ``` -## specmine (1.0) -Maintainer: Christopher Costa +## PopGenReport (3.0.0) +Maintainer: Bernd Gruber -1 error | 0 warnings | 0 notes +0 errors | 1 warning | 1 note ``` -checking package dependencies ... ERROR -Packages required but not available: ‘xcms’ ‘MAIT’ +checking whether package ‘PopGenReport’ can be installed ... WARNING +Found the following significant warnings: + Warning: namespace ‘DBI’ is not available and has been replaced +See ‘/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/checks/PopGenReport.Rcheck/00install.out’ for details. -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. +checking Rd cross-references ... NOTE +Package unavailable to check Rd xrefs: ‘ecodist’ ``` -## TVTB (1.2.0) -Maintainer: Kevin Rue-Albrecht -Bug reports: https://github.com/kevinrue/TVTB/issues +## POUMM (1.3.2) +Maintainer: Venelin Mitov -1 error | 1 warning | 1 note +1 error | 0 warnings | 0 notes ``` -checking tests ... ERROR - Running ‘testthat.R’ [15s/15s] -Running the tests in ‘tests/testthat.R’ failed. -Last 13 lines of output: - rs1426654 rs150379789 rs570906312 rs538198029 rs553496066 rs574775672 - TRUE TRUE FALSE FALSE TRUE FALSE - rs140666229 rs556950130 rs575303689 rs147513140 rs187525777 rs192454382 - TRUE FALSE TRUE TRUE FALSE FALSE - rs184818838 rs566886499 rs199924625 rs555872528 rs531820822 rs201353600 - FALSE FALSE FALSE FALSE FALSE FALSE - rs550201688 rs565338261 rs201239799 rs200461129 rs146726548 - FALSE FALSE FALSE FALSE TRUE - testthat results ================================================================ - OK: 229 SKIPPED: 0 FAILED: 2 - 1. Error: all signatures work to completion (@test_plotInfo-methods.R#25) - 2. Error: invalid metric/phenotype combination is detected (@test_plotInfo-methods.R#50) - - Error: testthat unit tests failed - Execution halted +checking whether package ‘POUMM’ can be installed ... ERROR +Installation failed. +See ‘/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/checks/POUMM.Rcheck/00install.out’ for details. +``` -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Overwriting INFO keys in data: -- REF -- HET -- ALT -- AAF -- MAF -Overwriting INFO keys in header: -- REF -- HET -- ALT -- AAF -- MAF -Quitting from lines 570-577 (Introduction.Rmd) -Error: processing vignette 'Introduction.Rmd' failed with diagnostics: -there is no package called 'EnsDb.Hsapiens.v75' -Execution halted +## specmine (1.0) +Maintainer: Christopher Costa +1 error | 0 warnings | 0 notes -checking package dependencies ... NOTE -Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’ ``` +checking package dependencies ... ERROR +Packages required but not available: ‘xcms’ ‘MAIT’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +``` + diff --git a/revdep/problems.md b/revdep/problems.md index 60c5ef0bf..8165e304b 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -4,135 +4,88 @@ |setting |value | |:--------|:----------------------------| -|version |R version 3.4.0 (2017-04-21) | +|version |R version 3.4.1 (2017-06-30) | |system |x86_64, darwin15.6.0 | |ui |X11 | |language |(EN) | |collate |en_US.UTF-8 | |tz |America/Indiana/Indianapolis | -|date |2017-06-07 | +|date |2017-08-02 | ## Packages -|package |* |version |date |source | -|:------------|:--|:-------|:----------|:-----------------------| -|broom | |0.4.2 |2017-02-13 |CRAN (R 3.4.0) | -|chemometrics | |1.4.2 |2017-03-17 |CRAN (R 3.4.0) | -|geosphere | |1.5-5 |2016-06-15 |CRAN (R 3.4.0) | -|GGally |* |1.3.1 |2017-06-07 |local (ggobi/ggally@NA) | -|ggplot2 | |2.2.1 |2016-12-30 |CRAN (R 3.4.0) | -|gtable | |0.2.0 |2016-02-26 |CRAN (R 3.4.0) | -|igraph | |1.0.1 |2015-06-26 |CRAN (R 3.4.0) | -|intergraph | |2.0-2 |2016-12-05 |CRAN (R 3.4.0) | -|mapproj | |1.2-4 |2015-08-03 |CRAN (R 3.4.0) | -|maps | |3.1.1 |2016-07-27 |CRAN (R 3.4.0) | -|network | |1.13.0 |2015-09-19 |CRAN (R 3.4.0) | -|packagedocs | |0.4.0 |2016-11-04 |CRAN (R 3.4.0) | -|plyr | |1.8.4 |2016-06-08 |CRAN (R 3.4.0) | -|progress | |1.1.2 |2016-12-14 |CRAN (R 3.4.0) | -|RColorBrewer | |1.1-2 |2014-12-07 |CRAN (R 3.4.0) | -|reshape | |0.8.6 |2016-10-21 |CRAN (R 3.4.0) | -|rmarkdown | |1.5 |2017-04-26 |CRAN (R 3.4.0) | -|roxygen2 | |6.0.1 |2017-02-06 |CRAN (R 3.4.0) | -|scagnostics | |0.2-4 |2012-11-05 |CRAN (R 3.4.0) | -|scales | |0.4.1 |2016-11-09 |CRAN (R 3.4.0) | -|sna | |2.4 |2016-08-08 |CRAN (R 3.4.0) | -|testthat | |1.0.2 |2016-04-23 |CRAN (R 3.4.0) | +|package |* |version |date |source | +|:------------|:--|:-------|:----------|:--------------| +|broom | |0.4.2 |2017-02-13 |CRAN (R 3.4.0) | +|chemometrics | |1.4.2 |2017-03-17 |CRAN (R 3.4.0) | +|geosphere | |1.5-5 |2016-06-15 |CRAN (R 3.4.0) | +|GGally |* |1.3.1 |2017-06-08 |CRAN (R 3.4.1) | +|ggplot2 | |2.2.1 |2016-12-30 |CRAN (R 3.4.0) | +|gtable | |0.2.0 |2016-02-26 |CRAN (R 3.4.0) | +|igraph | |1.1.2 |2017-07-21 |cran (@1.1.2) | +|intergraph | |2.0-2 |2016-12-05 |CRAN (R 3.4.0) | +|mapproj | |1.2-5 |2017-06-08 |CRAN (R 3.4.0) | +|maps | |3.2.0 |2017-06-08 |cran (@3.2.0) | +|network | |1.13.0 |2015-09-19 |CRAN (R 3.4.0) | +|packagedocs | |0.4.0 |2016-11-04 |CRAN (R 3.4.0) | +|plyr | |1.8.4 |2016-06-08 |CRAN (R 3.4.0) | +|progress | |1.1.2 |2016-12-14 |CRAN (R 3.4.0) | +|RColorBrewer | |1.1-2 |2014-12-07 |CRAN (R 3.4.0) | +|reshape | |0.8.6 |2016-10-21 |CRAN (R 3.4.0) | +|rmarkdown | |1.6 |2017-06-15 |CRAN (R 3.4.0) | +|roxygen2 | |6.0.1 |2017-02-06 |CRAN (R 3.4.0) | +|scagnostics | |0.2-4 |2012-11-05 |CRAN (R 3.4.0) | +|scales | |0.4.1 |2016-11-09 |CRAN (R 3.4.0) | +|sna | |2.4 |2016-08-08 |CRAN (R 3.4.0) | +|testthat | |1.0.2 |2016-04-23 |CRAN (R 3.4.0) | # Check results -5 packages with problems +6 packages with problems |package |version | errors| warnings| notes| |:--------------|:-------|------:|--------:|-----:| -|ggbio |1.24.0 | 1| 0| 5| +|eechidna |1.1 | 0| 1| 1| |MissingDataGUI |0.2-5 | 1| 0| 0| -|POUMM |1.2.2 | 0| 1| 0| +|nzelect |0.3.3 | 0| 1| 0| +|PopGenReport |3.0.0 | 0| 1| 1| +|POUMM |1.3.2 | 1| 0| 0| |specmine |1.0 | 1| 0| 0| -|TVTB |1.2.0 | 1| 1| 1| -## ggbio (1.24.0) -Maintainer: Michael Lawrence -Bug reports: https://github.com/tengfei/ggbio/issues +## eechidna (1.1) +Maintainer: Ben Marwick -1 error | 0 warnings | 5 notes +0 errors | 1 warning | 1 note ``` -checking examples ... ERROR -Running examples in ‘ggbio-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: autoplot -> ### Title: Generic autoplot function -> ### Aliases: autoplot autoplot,GRanges-method autoplot,GRangesList-method -> ### autoplot,IRanges-method autoplot,Seqinfo-method -> ### autoplot,BSgenome-method autoplot,GAlignments-method -... 416 lines ... -reduce alignemnts... -> -> -> ################################################### -> ### EnsDb -> ################################################### -> ## Fetching gene models from an EnsDb object. -> library(EnsDb.Hsapiens.v75) -Error in library(EnsDb.Hsapiens.v75) : - there is no package called 'EnsDb.Hsapiens.v75' +checking re-building of vignette outputs ... WARNING +Error in re-building vignettes: + ... + + nasa + +Warning: Removed 10 rows containing non-finite values (stat_smooth). +Warning: Removed 10 rows containing missing values (geom_point). + +Attaching package: 'readr' +... 8 lines ... + StateAb = col_character(), + GivenNm = col_character(), + Surname = col_character(), + PartyNm = col_character(), + PartyAb = col_character(), + ElectedOrder = col_integer() +) +Quitting from lines 154-171 (exploring-election-data2016.Rmd) +Error: processing vignette 'exploring-election-data2016.Rmd' failed with diagnostics: +Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'integer' Execution halted -checking package dependencies ... NOTE -Packages suggested but not available for checking: - ‘BSgenome.Hsapiens.UCSC.hg19’ ‘EnsDb.Hsapiens.v75’ - -checking top-level files ... NOTE -Non-standard file/directory found at top level: - ‘TODO.org’ - -checking dependencies in R code ... NOTE -Unexported objects imported by ':::' calls: - 'S4Vectors:::top_prenv' 'ggplot2:::add_ggplot' 'ggplot2:::cunion' - 'ggplot2:::rename_aes' 'ggplot2:::rescale01' - 'ggplot2:::set_last_plot' - See the note in ?`:::` about the use of this operator. - -checking R code for possible problems ... NOTE -.combineNames: no visible binding for global variable - '.layout_circle.stats' -Ideogram: no visible global function definition for 'data' -Ideogram: no visible binding for global variable 'ideoCyto' -Ideogram: no visible binding for global variable 'cytobands' -ScalePlot: no visible binding for global variable 'y' -ScalePlot2: no visible binding for global variable 'breaks' -ScalePlot2: no visible binding for global variable 'yend' -ScalePlot2: no visible binding for global variable 'y.text' -... 48 lines ... - .fragLength .layout_circle.stats .x breaks coefs cytobands data eds - fe fl gieStain ideoCyto indexProbesProcessed midpoint mt name read se - stepping sts value variable x xend y y.text y2 yend yend2 -Consider adding - importFrom("utils", "data") -to your NAMESPACE file. - -Found the following calls to data() loading into the global environment: -File ‘ggbio/R/ideogram.R’: - data(ideoCyto, package = "biovizBase") -See section ‘Good practice’ in ‘?data’. - -checking Rd line widths ... NOTE -Rd file 'autoplot-method.Rd': - \usage lines wider than 90 characters: - autoplot(object, ..., type = c("heatmap", "link", "pcp", "boxplot", "scatterplot.matrix"), pheno.plot = FALSE, - -Rd file 'geom_arrowrect-method.Rd': - \examples lines wider than 100 characters: - ggplot(gr) + geom_arrowrect(gr, stat = "stepping", aes(y = value, group = pair), group.selfish = FALSE) - -Rd file 'plotSingleChrom.Rd': - \usage lines wider than 90 characters: - plotIdeogram(obj, subchr = NULL, zoom.region = NULL, which = NULL, xlab, ylab, main, xlabel = - -These lines will be truncated in the PDF manual. +checking installed package size ... NOTE + installed size is 6.3Mb + sub-directories of 1Mb or more: + data 4.9Mb + doc 1.2Mb ``` ## MissingDataGUI (0.2-5) @@ -148,8 +101,8 @@ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ``` -## POUMM (1.2.2) -Maintainer: Venelin Mitov +## nzelect (0.3.3) +Maintainer: Peter Ellis 0 errors | 1 warning | 0 notes @@ -157,88 +110,49 @@ Maintainer: Venelin Mitov checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... - the condition has length > 1 and only the first element will be used -Warning in if (alpha == 0) { : - the condition has length > 1 and only the first element will be used -Warning in window.mcmc(mc$mcmc, start = start, end = end, thin = thinMCMC) : - end value not changed -Warning in if (alpha == 0) { : - the condition has length > 1 and only the first element will be used -... 8 lines ... - the condition has length > 1 and only the first element will be used -Warning in FUN(X[[i]], ...) : end value not changed -Warning in FUN(X[[i]], ...) : end value not changed -Warning in FUN(X[[i]], ...) : end value not changed -Warning in FUN(X[[i]], ...) : end value not changed -Warning in FUN(X[[i]], ...) : end value not changed -Warning in FUN(X[[i]], ...) : end value not changed -Quitting from lines 393-404 (UserGuide.Rmd) -Error: processing vignette 'UserGuide.Rmd' failed with diagnostics: -package 'adaptMCMC' not found +Quitting from lines 208-225 (README.Rmd) +Error: processing vignette 'README.Rmd' failed with diagnostics: +Evaluation error: votes, parties, and electorates should all be vectors of the same length. Execution halted + ``` -## specmine (1.0) -Maintainer: Christopher Costa +## PopGenReport (3.0.0) +Maintainer: Bernd Gruber -1 error | 0 warnings | 0 notes +0 errors | 1 warning | 1 note ``` -checking package dependencies ... ERROR -Packages required but not available: ‘xcms’ ‘MAIT’ +checking whether package ‘PopGenReport’ can be installed ... WARNING +Found the following significant warnings: + Warning: namespace ‘DBI’ is not available and has been replaced +See ‘/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/checks/PopGenReport.Rcheck/00install.out’ for details. -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. +checking Rd cross-references ... NOTE +Package unavailable to check Rd xrefs: ‘ecodist’ ``` -## TVTB (1.2.0) -Maintainer: Kevin Rue-Albrecht -Bug reports: https://github.com/kevinrue/TVTB/issues +## POUMM (1.3.2) +Maintainer: Venelin Mitov -1 error | 1 warning | 1 note +1 error | 0 warnings | 0 notes ``` -checking tests ... ERROR - Running ‘testthat.R’ [14s/15s] -Running the tests in ‘tests/testthat.R’ failed. -Last 13 lines of output: - rs1426654 rs150379789 rs570906312 rs538198029 rs553496066 rs574775672 - TRUE TRUE FALSE FALSE TRUE FALSE - rs140666229 rs556950130 rs575303689 rs147513140 rs187525777 rs192454382 - TRUE FALSE TRUE TRUE FALSE FALSE - rs184818838 rs566886499 rs199924625 rs555872528 rs531820822 rs201353600 - FALSE FALSE FALSE FALSE FALSE FALSE - rs550201688 rs565338261 rs201239799 rs200461129 rs146726548 - FALSE FALSE FALSE FALSE TRUE - testthat results ================================================================ - OK: 229 SKIPPED: 0 FAILED: 2 - 1. Error: all signatures work to completion (@test_plotInfo-methods.R#25) - 2. Error: invalid metric/phenotype combination is detected (@test_plotInfo-methods.R#50) - - Error: testthat unit tests failed - Execution halted +checking whether package ‘POUMM’ can be installed ... ERROR +Installation failed. +See ‘/Users/barret/odrive/AmazonCloudDrive/git/R/ggobi_org/ggally/ggally/revdep/checks/POUMM.Rcheck/00install.out’ for details. +``` -checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Overwriting INFO keys in data: -- REF -- HET -- ALT -- AAF -- MAF -Overwriting INFO keys in header: -- REF -- HET -- ALT -- AAF -- MAF -Quitting from lines 570-577 (Introduction.Rmd) -Error: processing vignette 'Introduction.Rmd' failed with diagnostics: -there is no package called 'EnsDb.Hsapiens.v75' -Execution halted +## specmine (1.0) +Maintainer: Christopher Costa +1 error | 0 warnings | 0 notes + +``` +checking package dependencies ... ERROR +Packages required but not available: ‘xcms’ ‘MAIT’ -checking package dependencies ... NOTE -Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’ +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. ``` + diff --git a/revdep/timing.md b/revdep/timing.md index ae6f2239d..13279d570 100644 --- a/revdep/timing.md +++ b/revdep/timing.md @@ -1,47 +1,50 @@ # Check times -| |package |version | check_time| -|:--|:-------------------|:-------|----------:| -|17 |MAST |1.2.1 | 381.3| -|19 |MCbiclust |1.0.1 | 346.9| -|14 |isomiRs |1.4.0 | 285.9| -|7 |ggbio |1.24.0 | 269.2| -|23 |Pi |1.4.0 | 258.5| -|38 |TVTB |1.2.0 | 209.8| -|34 |spup |0.1-0 | 174.5| -|29 |robustbase |0.92-7 | 150.1| -|18 |mbgraphic |1.0.0 | 146.7| -|39 |userfriendlyscience |0.6-1 | 118.9| -|21 |mlrMBO |1.1.0 | 118.2| -|28 |robCompositions |2.0.3 | 107.2| -|25 |PopGenReport |3.0.0 | 105| -|16 |LANDD |1.1.0 | 101.1| -|5 |eechidna |1.1 | 99.7| -|12 |ICtest |0.2 | 90.8| -|11 |httk |1.5 | 88.7| -|26 |POUMM |1.2.2 | 88.7| -|9 |ggmcmc |1.1 | 84| -|2 |BAS |1.4.6 | 68.6| -|13 |imageData |0.1-26 | 68.1| -|41 |vortexR |1.1.4 | 63.8| -|31 |rwty |1.0.1 | 63.4| -|8 |ggCompNet |0.1.0 | 54.2| -|40 |vdmR |0.2.3 | 53.2| -|3 |clustrd |1.2.0 | 52.5| -|24 |plotly |4.7.0 | 51.3| -|36 |texmex |2.3 | 48| -|35 |svdvis |0.1 | 46.5| -|15 |jmv |0.7.3.5 | 45.6| -|32 |SHELF |1.2.3 | 43.9| -|22 |ParamHelpers |1.10 | 43.4| -|30 |rrr |1.0.0 | 43| -|1 |BANFF |2.0 | 42.4| -|37 |toaster |0.5.5 | 35.7| -|10 |gsynth |1.0.3 | 33.2| -|4 |DescribeDisplay |0.2.5 | 27.3| -|6 |freqparcoord |1.0.1 | 25.5| -|27 |qualvar |0.1.0 | 18.4| -|33 |specmine |1.0 | 1.4| -|20 |MissingDataGUI |0.2-5 | 1.2| +| |package |version | check_time| +|:--|:---------------------|:-------|----------:| +|25 |Pi |1.4.0 | 15545.1| +|8 |ggbio |1.24.1 | 433.1| +|18 |MAST |1.2.1 | 320.9| +|20 |MCbiclust |1.0.1 | 319| +|37 |spup |0.1-1 | 284.8| +|15 |isomiRs |1.4.0 | 253.4| +|41 |TVTB |1.2.0 | 234.7| +|32 |robustbase |0.92-7 | 144.4| +|19 |mbgraphic |1.0.0 | 124.4| +|27 |PopGenReport |3.0.0 | 108.6| +|31 |robCompositions |2.0.5 | 106.2| +|42 |userfriendlyscience |0.6-1 | 106| +|22 |mlrMBO |1.1.0 | 97.4| +|17 |LANDD |1.1.0 | 88.8| +|13 |ICtest |0.3 | 88.5| +|3 |CINNA |1.0.0 | 87.2| +|12 |httk |1.7 | 83.4| +|10 |ggmcmc |1.1 | 80| +|6 |eechidna |1.1 | 67.9| +|2 |BAS |1.4.6 | 65.9| +|44 |vortexR |1.1.4 | 62| +|14 |imageData |0.1-26 | 61.5| +|34 |rwty |1.0.1 | 60.1| +|30 |randomForestExplainer |0.9 | 56| +|9 |ggCompNet |0.1.0 | 52.2| +|4 |clustrd |1.2.0 | 50.8| +|43 |vdmR |0.2.4 | 47.5| +|26 |plotly |4.7.1 | 46| +|39 |texmex |2.3 | 45.7| +|38 |svdvis |0.1 | 44.6| +|16 |jmv |0.7.3.5 | 44.1| +|33 |rrr |1.0.0 | 41.5| +|35 |SHELF |1.2.3 | 41.2| +|1 |BANFF |2.0 | 40.8| +|24 |ParamHelpers |1.10 | 32| +|40 |toaster |0.5.5 | 32| +|11 |gsynth |1.0.3 | 30.3| +|23 |nzelect |0.3.3 | 28.3| +|5 |DescribeDisplay |0.2.5 | 25.2| +|7 |freqparcoord |1.0.1 | 24.9| +|29 |qualvar |0.1.0 | 19.8| +|28 |POUMM |1.3.2 | 2.8| +|21 |MissingDataGUI |0.2-5 | 1.4| +|36 |specmine |1.0 | 1.4| diff --git a/tests/testthat/test-ggnet.R b/tests/testthat/test-ggnet.R index fccc79569..b412c0955 100644 --- a/tests/testthat/test-ggnet.R +++ b/tests/testthat/test-ggnet.R @@ -226,16 +226,16 @@ test_that("examples", { expect_error(ggnet(network(data.frame(1:2, 3:4), multiple = TRUE)), "multiplex graphs") ### --- test igraph functionality - - # test igraph conversion - p <- ggnet(asIgraph(n)) - expect_null(p$guides$colour) - expect_equal(length(p$layers), 2) - - # test igraph degree - library(igraph) - ggnet(n, weight = "degree") - - expect_true(TRUE) + if (requireNamespace("igraph", quietly = TRUE)) { + library(igraph) + # test igraph conversion + p <- ggnet(asIgraph(n)) + expect_null(p$guides$colour) + expect_equal(length(p$layers), 2) + + # test igraph degree + ggnet(n, weight = "degree") + expect_true(TRUE) + } }) diff --git a/tests/testthat/test-ggnet2.R b/tests/testthat/test-ggnet2.R index 1032874e3..b97c08e01 100644 --- a/tests/testthat/test-ggnet2.R +++ b/tests/testthat/test-ggnet2.R @@ -260,15 +260,16 @@ test_that("examples", { expect_error(ggnet2(network(data.frame(1:2, 3:4), multiple = TRUE)), "multiplex graphs") ### --- test igraph functionality + if (requireNamespace("igraph", quietly = TRUE)) { + library(igraph) + # test igraph conversion + p <- ggnet2(asIgraph(n), color = "group") + expect_null(p$guides$colour) - # test igraph conversion - p <- ggnet2(asIgraph(n), color = "group") - expect_null(p$guides$colour) + # test igraph degree + ggnet2(n, size = "degree") - # test igraph degree - library(igraph) - ggnet2(n, size = "degree") - - expect_true(TRUE) + expect_true(TRUE) + } }) diff --git a/tests/testthat/test-ggnetworkmap.R b/tests/testthat/test-ggnetworkmap.R index a619a51f6..1b567526f 100644 --- a/tests/testthat/test-ggnetworkmap.R +++ b/tests/testthat/test-ggnetworkmap.R @@ -198,9 +198,13 @@ test_that("network coercion", { ### --- test igraph functionality test_that("igraph conversion", { - n <- asIgraph(flights) - p <- ggnetworkmap(net = n) - expect_equal(length(p$layers), 2) + + if (requireNamespace("igraph", quietly = TRUE)) { + library(igraph) + n <- asIgraph(flights) + p <- ggnetworkmap(net = n) + expect_equal(length(p$layers), 2) + } }) expect_true(TRUE) diff --git a/tests/testthat/test-ggparcoord.R b/tests/testthat/test-ggparcoord.R index 4fd06959e..1cd6e0565 100644 --- a/tests/testthat/test-ggparcoord.R +++ b/tests/testthat/test-ggparcoord.R @@ -99,6 +99,15 @@ test_that("stops", { "invalid value for 'boxplot'" ) + expect_error( + ggparcoord(data = diamonds.samp, columns = c(1, 5:10), groupColumn = 2, shadeBox = c(1, 2)), + "invalid value for 'shadeBox'; must be a single color" + ) + expect_error( + ggparcoord(data = diamonds.samp, columns = c(1, 5:10), groupColumn = 2, shadeBox = "notacolor"), + "invalid value for 'shadeBox'; must be a valid R color" + ) + expect_error( ggparcoord(diamonds.samp, columns = c(1, 5:10), groupColumn = 2, splineFactor = NULL), "invalid value for 'splineFactor'" diff --git a/tests/testthat/test-zzz_ggpairs.R b/tests/testthat/test-zzz_ggpairs.R index 77269759c..2a00356a2 100644 --- a/tests/testthat/test-zzz_ggpairs.R +++ b/tests/testthat/test-zzz_ggpairs.R @@ -202,15 +202,6 @@ test_that("stops", { ggduo(tips, columnsY = 1:3, columnLabelsY = c("A", "B", "C", "Extra")) }, "The length of the 'columnLabelsY' does not match the length of the 'columnsY'") # nolint - dt <- tips - colnames(dt)[3] <- "1" - expect_warning({ - pm <- ggpairs(dt, lower = facethistBindwidth1) - }, "Data column name is numeric") # nolint - expect_warning({ - pm <- ggduo(dt, types = facethistBindwidth1Duo) - }, "Data column name is numeric") # nolint - expect_error({ ggpairs(tips, upper = c("not_a_list")) }, "'upper' is not a list") # nolint diff --git a/tests/testthat/test-zzzz_lintr.R b/tests/testthat/test-zzzz_lintr.R deleted file mode 100644 index b66a2e358..000000000 --- a/tests/testthat/test-zzzz_lintr.R +++ /dev/null @@ -1,8 +0,0 @@ - -# https://github.com/jimhester/lintr -if (requireNamespace("lintr", quietly = TRUE)) { - context("lints") - test_that("Package Style", { - lintr::expect_lint_free(cache = FALSE) - }) -}