############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SISPA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SISPA_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SISPA.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘SISPA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SISPA’ version ‘1.30.0’ * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘SISPA’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Version 0.99.1: Original Cannot process chunk/lines: Version 0.99.2: Bugfix: - Example ERROR fixed, generates ERROR message when no change points are identified. Cannot process chunk/lines: Version 0.99.3: Bugfix: - Example ERROR fixed, generates ERROR message when no change points are identified. Cannot process chunk/lines: Version 0.99.4: Bugfix: - Example ERROR fixed, generates ERROR message when no change points are identified. Cannot process chunk/lines: Version 1.1.0 First Release version Cannot process chunk/lines: Version 1.1.1: New Features: - For more than 3 genes, standard zscore is computed instead of GSVA enrichment scores - For sample size less than 3, zscore can not be computed, program generates an error - SISPA can now run on a single data type or any combination of two numeric data types - changepoint R method options as input parameters - implemented ggplot to create barplot in the freqplot function - Updated vignettes as pdf file to perform 1D and 2D SISPA analysis - SISPA.R numeric ERROR fixed Cannot process chunk/lines: Version 1.1.2: New Features: - cptSamples.R changepoint ERROR fixed Cannot process chunk/lines: Bhakti Dwivedi and Jeanne Kowalski Cannot process chunk/lines: The Winship Cancer Institute, Emory University Cannot process chunk/lines: https://bbisr.winship.emory.edu/ * checking R 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 ... NOTE cptSamples : cptsPlot: no visible global function definition for ‘abline’ cptSamples : cptsPlot: no visible global function definition for ‘text’ Undefined global functions or variables: abline text Consider adding importFrom("graphics", "abline", "text") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘SISPA-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: freqplot > ### Title: A plotting function for SISPA sample identifiers > ### Aliases: freqplot > > ### ** Examples > > samples <- c("s1","s2","s3","s4","s5","s6","s7","s8","s9","s10") > zscores <- c(3.83,2.70,2.67,2.31,1.70,1.25,-0.42,-1.01,-2.43,-3.37) > changepoints <- c(1,1,1,2,2,3,3,NA,NA,NA) > sample_groups <- c(1,1,1,0,0,0,0,0,0,0) > my.data = data.frame(samples,zscores,changepoints,sample_groups) > freqplot(my.data) Error in value[[3L]](cond) : The melt generic in data.table has been passed a data.frame, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(count_data) or as.data.table(count_data). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is deprecated and you should be migrating your code away from using it. Calls: freqplot ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘SISPA.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/SISPA.Rcheck/00check.log’ for details.