############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iSEEhex.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iSEEhex_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/iSEEhex.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘iSEEhex/DESCRIPTION’ ... OK * this is package ‘iSEEhex’ version ‘1.7.0’ * 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 ‘iSEEhex’ 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘iSEEhex-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: ReducedDimensionHexPlot-class > ### Title: The ReducedDimensionHexPlot class > ### Aliases: ReducedDimensionHexPlot-class ReducedDimensionHexPlot > ### initialize,ReducedDimensionHexPlot-method > ### .fullName,ReducedDimensionHexPlot-method > ### .panelColor,ReducedDimensionHexPlot-method > ### .createObservers,ReducedDimensionHexPlot-method > ### .hideInterface,ReducedDimensionHexPlot-method > ### .defineVisualShapeInterface,ReducedDimensionHexPlot-method > ### .defineVisualSizeInterface,ReducedDimensionHexPlot-method > ### .defineVisualOtherInterface,ReducedDimensionHexPlot-method > ### .generateDotPlot,ReducedDimensionHexPlot-method > ### .definePanelTour,ReducedDimensionHexPlot-method > ### .getDotPlotColorHelp,ReducedDimensionHexPlot-method > ### .allowableColorByDataChoices,ReducedDimensionHexPlot-method > > ### ** Examples > > library(scRNAseq) > > # Example data ---- > sce <- ReprocessedAllenData(assays="tophat_counts") Error in H5Fopen(fpath) : HDF5. File accessibility. Unable to open file. Calls: ReprocessedAllenData ... altReadObject -> FUN -> readObject -> meth -> H5Fopen Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 1 ERROR See ‘/Users/biocbuild/bbs-3.20-bioc/meat/iSEEhex.Rcheck/00check.log’ for details.