- using R Under development (unstable) (2025-02-23 r87804)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 19.1.7 (1+b1)
Debian flang-new version 19.1.7 (1+b1)
- 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 the install log 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 ... [2s/2s] OK
- checking whether the package can be unloaded cleanly ... [2s/2s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
- checking whether the namespace can be unloaded cleanly ... [2s/3s] 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 ... [12s/17s] 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 ... [15s/23s] 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
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Warning in file(con, "w") :
cannot open file '/home/hornik/tmp/R.check/r-devel-clang/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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
run_qc 5.972 0.143 9.13
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [3s/3s] OK
Running ‘testthat.R’ [3s/3s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [9s/13s] 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