* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/rgenie.Rcheck’ * using R Under development (unstable) (2021-05-10 r80282) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘rgenie/DESCRIPTION’ ... OK * this is package ‘rgenie’ version ‘1.0.0’ * 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 ‘rgenie’ can be installed ... 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 ... OK * 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 ... NOTE Namespaces in Imports field not imported from: ‘stats’ ‘tibble’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [11s/11s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [25s/25s] OK * checking examples with --run-donttest ... ERROR Running examples in ‘rgenie-Ex.R’ failed The error most likely occurred in: > ### Name: deletion_analysis > ### Title: Alignment-based GenIE analysis > ### Aliases: deletion_analysis > > ### ** Examples > > # Note: to run an analysis you need BAM files from a GenIE experiment. > # An example is available for download using download_example(). > > ## No test: > download_example(dir = "~/genie_example", name = "MUL1") Example data for MUL1 is already present. To overwrite it, set overwrite = TRUE. > # Data are downloaded and we can run an rgenie analysis > setwd("~/genie_example/MUL1/") > regions = readr::read_tsv("mul1.genie_regions.tsv") Error: 'mul1.genie_regions.tsv' does not exist in current working directory ('/data/blackswan/ripley/genie_example/MUL1'). Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [19s/20s] OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/data/blackswan/ripley/R/packages/tests-devel/rgenie.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 1:40.27, 94.38 + 5.31