* using log directory 'd:/Rcompile/CRANpkg/local/4.4/gimap.Rcheck' * using R version 4.4.3 (2025-02-28 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'gimap/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'gimap' version '1.1.1' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'gimap' 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 ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [2s] OK * checking whether the package can be loaded with stated dependencies ... [2s] OK * checking whether the package can be unloaded cleanly ... [2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s] OK * checking whether the namespace can be unloaded cleanly ... [3s] OK * checking loading without being on the library search path ... [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 ... [8s] OK * checking Rd files ... [1s] 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [65s] ERROR Running examples in 'gimap-Ex.R' failed The error most likely occurred in: > ### Name: setup_data > ### Title: Making a new gimap dataset > ### Aliases: setup_data > > ### ** Examples > > > counts <- get_example_data("count", data_dir = tempdir()) %>% + 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% Error in get_figshare(file_name = file_name, item = "28264271", output_dir = data_dir) : Gateway Timeout (HTTP 504). Calls: %>% ... -> get_example_data -> get_figshare -> Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... [3s] OK Running 'testthat.R' [3s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [14s] ERROR Error(s) in re-building vignettes: --- re-building 'quick-start.Rmd' using rmarkdown File output_timepoints/exp_v_obs_scatter.png not found in resource path Error: processing vignette 'quick-start.Rmd' failed with diagnostics: pandoc document conversion failed with error 99 --- failed re-building 'quick-start.Rmd' --- re-building 'timepoint-example.Rmd' using rmarkdown Warning in get_engine(options$engine) : Unknown language engine 'reval' (must be registered via knit_engines$set()). File output_timepoints/exp_v_obs_scatter.png not found in resource path Error: processing vignette 'timepoint-example.Rmd' failed with diagnostics: pandoc document conversion failed with error 99 --- failed re-building 'timepoint-example.Rmd' --- re-building 'treatment_example.Rmd' using rmarkdown File output_treatment/exp_v_obs_scatter.png not found in resource path Error: processing vignette 'treatment_example.Rmd' failed with diagnostics: pandoc document conversion failed with error 99 --- failed re-building 'treatment_example.Rmd' SUMMARY: processing the following files failed: 'quick-start.Rmd' 'timepoint-example.Rmd' 'treatment_example.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [18s] OK * checking HTML version of manual ... [6s] OK * DONE Status: 2 ERRORs