############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:orthos.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings orthos_1.4.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/orthos.Rcheck’ * using R version 4.4.3 (2025-02-28) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘orthos/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘orthos’ version ‘1.4.1’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘orthos’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/Users/biocbuild/bbs-3.20-bioc/meat/orthos.Rcheck/00install.out’ 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 ... 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 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 line endings in shell scripts ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘orthos-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: decomposeVar > ### Title: Decompose input contrasts to decoded and residual fractions > ### Aliases: decomposeVar > > ### ** Examples > > MKL1_human <- readRDS(system.file("extdata", "GSE215150_MKL1_Human.rds", + package = "orthos")) > > # Specifying M, treatm and cntr: > dec_MKL1_human <- decomposeVar(M = MKL1_human, treatm = c(2, 3), cntr = c(1, 1), + organism = "Human", verbose = FALSE) Error in vapply(urls, FUN = function(url) { : values must be length 1, but FUN(X[[1]]) result is length 0 Calls: decomposeVar ... -> getInfoOnIds -> getInfoOnIds -> getSize -> vapply 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: but FUN(X[[1]]) result is length 0 Backtrace: ▆ 1. └─orthos:::.readGeneInformation("Human", mustWork = FALSE) at test-queryWithContrasts.R:48:5 2. └─orthosData::GetorthosContrastDB(...) 3. ├─AnnotationHub::getInfoOnIds(rds_hubObj) 4. └─AnnotationHub::getInfoOnIds(rds_hubObj) 5. ├─AnnotationHub::getInfoOnIds(hub, ids) 6. └─AnnotationHub::getInfoOnIds(hub, ids) 7. └─AnnotationHub:::getSize(hub, res) 8. └─base::vapply(...) [ FAIL 3 | WARN 2 | SKIP 1 | PASS 164 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/orthos.Rcheck/00check.log’ for details.