[ Started: 2025-10-13 21:20:49 CEST ] [ dorothea v1.20.0 for BioC-3.21 from https://git.bioconductor.org/packages/dorothea@RELEASE_3_21 (109bfa1 2025-04-15 10:14:54) ] * using log directory ‘/mnt/disk0/build/bioc-check/dorothea/bioc-3.21/2025-10-13_2117/dorothea/dorothea.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘dorothea/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘dorothea’ version ‘1.20.0’ * 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 ‘dorothea’ can be installed ... OK * checking installed package size ... INFO installed size is 35.7Mb sub-directories of 1Mb or more: data 5.0Mb doc 2.4Mb extdata 17.3Mb help 1.3Mb testdata 9.4Mb * 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... OK * checking Rd files ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... 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 ... ERROR Running examples in ‘dorothea-Ex.R’ failed The error most likely occurred in: > ### Name: run_viper > ### Title: VIPER wrapper > ### Aliases: run_viper > > ### ** Examples > > # use example gene expression matrix from bcellViper package > library(bcellViper) Loading required package: Biobase Loading required package: BiocGenerics Loading required package: generics Attaching package: ‘generics’ The following objects are masked from ‘package:base’: as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > data(bcellViper, package = "bcellViper") > # acessing (human) dorothea regulons > # for mouse regulons: data(dorothea_mm, package = "dorothea") > data(dorothea_hs, package = "dorothea") > # run viper > tf_activities <- run_viper(dset, dorothea_hs, + options = list(method = "scale", minsize = 4, + eset.filter = FALSE, cores = 1, + verbose = FALSE)) Warning in run_viper.matrix(Biobase::exprs(input), regulons = regulons, : This function is deprecated, please check the package decoupleR to infer activities. Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/kernlab/libs/kernlab.so': libRblas.so: cannot open shared object file: No such file or directory Calls: run_viper ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 19. ├─tibble::rownames_to_column(., "source") 20. ├─base::as.data.frame(.) 21. └─base::loadNamespace(x) 22. ├─base::namespaceImportFrom(...) 23. │ └─base::asNamespace(ns) 24. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 25. ├─base::namespaceImportFrom(...) 26. │ └─base::asNamespace(ns) 27. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 28. └─base::library.dynam(lib, package, package.lib) 29. └─base::dyn.load(file, DLLpath = DLLpath, ...) [ FAIL 5 | WARN 4 | SKIP 0 | PASS 4 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' call not declared from: ‘ggplot2’ * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 NOTE See ‘/mnt/disk0/build/bioc-check/dorothea/bioc-3.21/2025-10-13_2117/dorothea/dorothea.Rcheck/00check.log’ for details. [ Finished: 2025-10-13 21:22:48 CEST ]