* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/IPDfromKM.Rcheck’ * using R Under development (unstable) (2024-10-11 r87226) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7) GNU Fortran (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7) * running under: Fedora Linux 38 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘IPDfromKM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘IPDfromKM’ version ‘0.1.10’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘IPDfromKM’ can be installed ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [10s/10s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... OK * checking examples with --run-donttest ... ERROR Running examples in ‘IPDfromKM-Ex.R’ failed The error most likely occurred in: > ### Name: getpoints > ### Title: Extract the coordinates from Kaplan-Meier(K-M) curves by > ### mouse-clicks > ### Aliases: getpoints > > ### ** Examples > > str(imgexp) num [1:348, 1:437] 1 1 1 1 1 1 1 1 1 1 ... > ## No test: > > ## Extract the coordinates from Kaplan-Meier(K-M) curves by mouse-clicks. > ## The K-M curve should be in the format of bitmap images. The input f should be either > ## the pathway to the image file, or the bitmap digital image itself. > ## Example: extract coordinates from the sample bitmap digital image (imgexp) > plot.new() > rasterImage(imgexp, 0, 0, 1, 1) > ## User need to use mouse-clicks to decide the positions of coordinates, > ## and the points want to extract. > df <- getpoints(imgexp,0,60,0,100) You need to define the points on the x and y axis according to your input x1,x2,y1,y2. Click in the order of left x-axis point (x1), right x-axis point(x2), lower y-axis point(y1), and upper y-axis point(y2). Mouse click on the K-M curve to take the points of interest. The points will only be labled when you finish all the clicks. Error in model.frame.default(formula = c(x1, x2) ~ c(x), drop.unused.levels = TRUE) : invalid type (NULL) for variable 'c(x)' Calls: getpoints ... lm -> eval -> eval -> -> model.frame.default Execution halted * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR See ‘/data/blackswan/ripley/R/packages/tests-devel/IPDfromKM.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 1:02.89, 54.84 + 7.76