* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gimap.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (Debian 14.2.0-16) 14.2.0 GNU Fortran (Debian 14.2.0-16) 14.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘gimap/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gimap’ version ‘1.0.2’ * 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 ‘gimap’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/gimap-00install.html' for details. * checking package directory ... OK * checking for future file timestamps ... 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [2s/2s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [2s/2s] OK * checking loading without being on the library search path ... [2s/3s] OK * checking use of S3 registration ... 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/16s] OK * checking Rd files ... [0s/1s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [14s/20s] ERROR Running examples in ‘gimap-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: setup_data > ### Title: Making a new gimap dataset > ### Aliases: setup_data > > ### ** Examples > > > counts <- get_example_data("count") %>% + dplyr::select(c( + "Day00_RepA", "Day05_RepA", "Day22_RepA", "Day22_RepB", + "Day22_RepC" + )) %>% + as.matrix() Downloading: 1.4 kB Downloading: 1.4 kB Downloading: 1.4 kB Downloading: 1.4 kB Downloading: PP_pgPEN_HeLa_counts.txt | | | 0% | |======================================================================| 100% | | | 0% | | | 1% | |== | 3% | |=== | 4% | |==== | 6% | |===== | 7% | |======= | 10% | |========= | 14% | |========== | 14% | |=========== | 16% | |============ | 17% | |============= | 18% | |============= | 19% | |============== | 20% | |================ | 23% | |================= | 24% | |================== | 26% | |=================== | 27% | |=================== | 28% | |====================== | 32% | |========================= | 35% | |============================ | 39% | |============================== | 43% | |================================= | 47% | |=================================== | 50% | |====================================== | 54% | |======================================== | 58% | |========================================== | 60% | |=========================================== | 61% | |============================================ | 62% | |============================================= | 64% | |============================================== | 65% | |=============================================== | 66% | |=============================================== | 67% | |================================================ | 68% | |=================================================== | 72% | |====================================================== | 78% | |========================================================== | 83% | |=========================================================== | 84% | |============================================================ | 85% | |============================================================= | 87% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 90% | |================================================================ | 92% | |================================================================= | 92% | |================================================================== | 94% | |================================================================== | 95% | |======================================================================| 100% Warning in file(con, "w") : cannot open file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/gimap/extdata/PP_pgPEN_HeLa_counts.txt': Read-only file system Error in file(con, "w") : cannot open the connection Calls: %>% ... get_example_data -> get_figshare -> writeLines -> file Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [3s/3s] OK Running ‘testthat.R’ [2s/3s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [9s/12s] OK * checking PDF version of manual ... [5s/6s] OK * checking HTML version of manual ... [1s/2s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 ERROR