* using log directory ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gimap.Rcheck’
* using R version 4.4.3 RC (2025-02-20 r87814)
* 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-patched-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/2s] OK
* checking whether the package can be unloaded cleanly ... [1s/2s] 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/2s] 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/13s] OK
* checking Rd files ... [0s/0s] 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/19s] 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-patched-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