############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no zellkonverter_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/zellkonverter.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.1 * using session charset: UTF-8 * using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’ * checking for file ‘zellkonverter/DESCRIPTION’ ... OK * this is package ‘zellkonverter’ version ‘1.14.0’ * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘zellkonverter’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/zellkonverter.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package 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 ... SKIPPED * 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’ ... SKIPPED * checking examples ... SKIPPED * checking for unstated dependencies in ‘longtests’ ... OK * checking tests in ‘longtests’ ... Running ‘testthat.R’ ERROR Running the tests in ‘longtests/testthat.R’ failed. Last 13 lines of output: ▆ 1. ├─BiocFileCache::bfcrpath(cache, "https://storage.googleapis.com/gtex_analysis_v9/snrna_seq_data/GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad") at test-gtex_8tissues.R:6:1 2. └─BiocFileCache::bfcrpath(cache, "https://storage.googleapis.com/gtex_analysis_v9/snrna_seq_data/GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad") ── Failure ('test-pegasus_marrow.R:37:5'): SCE is valid ──────────────────────── varm names not identical to `correct_names`. Lengths differ: 4 is not 5 Backtrace: ▆ 1. └─zellkonverter:::validateH5ADSCE(sce, names, missing) at test-pegasus_marrow.R:37:5 2. └─zellkonverter:::.names_validator(...) 3. └─testthat::expect_identical(actual_names, correct_names, label = label) [ FAIL 2 | WARN 18 | SKIP 0 | PASS 178 ] Error: Test failures Execution halted * DONE Status: 1 ERROR, 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/zellkonverter.Rcheck/00check.log’ for details.