* using log directory 'd:/Rcompile/CRANpkg/local/4.5/enrichR.Rcheck' * using R Under development (unstable) (2024-08-15 r87022 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'enrichR/DESCRIPTION' ... OK * this is package 'enrichR' version '3.2' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'enrichR' can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-windows-x86_64/enrichR-00install.html' for details. * 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 ... [3s] 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 ... [1s] OK * checking whether the namespace can be unloaded cleanly ... [1s] OK * checking loading without being on the library search path ... [3s] OK * checking whether startup messages can be suppressed ... [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 ... [4s] OK * checking Rd files ... [0s] OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: plotEnrich.Rd: ggplot Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ... [0s] 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 ... [125s] ERROR Running examples in 'enrichR-Ex.R' failed The error most likely occurred in: > ### Name: plotEnrich > ### Title: plotEnrich > ### Aliases: plotEnrich > > ### ** Examples > > if (getOption("enrichR.live")) { + dbs <- listEnrichrDbs() + enrichRLive <- TRUE + if (is.null(dbs)) enrichRLive <- FALSE + dbs <- c("GO_Molecular_Function_2018", "GO_Cellular_Component_2018", + "GO_Biological_Process_2018") + enriched <- enrichr(c("Runx1", "Gfi1", "Gfi1b", "Spi1", "Gata1", "Kdr"), dbs) + # Plot top 20 terms from "GO_Biological_Process_2018" and ordered by P-value + if (enrichRLive) { + plotEnrich(enriched[[3]], showTerms = 20, numChar = 50, y = "Count", + orderBy = "P.value") + } + } Uploading data to Enrichr... Done. Querying GO_Molecular_Function_2018... Done. Querying GO_Cellular_Component_2018... Done. Querying GO_Biological_Process_2018... Done. Parsing results... Done. Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 2, 0 Calls: plotEnrich ... .enrichment_prep_df -> cbind -> cbind -> data.frame Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [66s] ERROR Error(s) in re-building vignettes: --- re-building 'enrichR.Rmd' using rmarkdown Quitting from lines 96-99 [unnamed-chunk-11] (enrichR.Rmd) Error: processing vignette 'enrichR.Rmd' failed with diagnostics: arguments imply differing number of rows: 2, 0 --- failed re-building 'enrichR.Rmd' SUMMARY: processing the following file failed: 'enrichR.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [20s] OK * checking HTML version of manual ... [2s] OK * DONE Status: 2 ERRORs, 1 NOTE