• using R Under development (unstable) (2025-08-24 r88696)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.7 (3+b2)     Debian flang-new version 19.1.7 (3+b2)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘rliger/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘rliger’ version ‘2.2.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/3s] OK
• 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 ‘rliger’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘Debian clang version 19.1.7 (3+b2)’
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [10s/14s] OK
• checking whether the package can be loaded with stated dependencies ... [10s/13s] OK
• checking whether the package can be unloaded cleanly ... [11s/14s] OK
• checking whether the namespace can be loaded with stated dependencies ... [10s/12s] OK
• checking whether the namespace can be unloaded cleanly ... [10s/12s] OK
• checking loading without being on the library search path ... [10s/12s] OK
• checking whether startup messages can be suppressed ... [10s/13s] 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 ... [79s/94s] OK
• checking Rd files ... [2s/2s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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 ... [11s/13s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [83s/92s] ERROR Running examples in ‘rliger-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: read10XH5 > ### Title: Read 10X HDF5 file > ### Aliases: read10XH5 read10XH5Mem read10XH5Delay > > ### ** Examples > > matrix <- read10XH5( + filename = system.file("extdata/ctrl.h5", package = "rliger"), + inMemory = TRUE + ) > class(matrix) # Should show dgCMatrix [1] "dgCMatrix" attr(,"package") [1] "Matrix" > if (requireNamespace("HDF5Array", quietly = TRUE)) { + matrix <- read10XH5( + filename = system.file("extdata/ctrl.h5", package = "rliger"), + inMemory = FALSE + ) + print(class(matrix)) # Should show TENxMatrix + } Failed with error: ‘unused argument (quitely = TRUE)’ Error in `read10XH5Delay()`: ✖ Package HDF5Array is required for reading 10X H5 data into   DelayedArray. ℹ Please install with `BiocManager::install('HDF5Array')`. Backtrace:     ▆  1. └─rliger::read10XH5(...)  2. └─rliger::read10XH5Delay(filename, useNames, featureMakeUniq)  3. └─cli::cli_abort(...)  4. └─rlang::abort(...) Execution halted Examples with CPU (user + system) or elapsed time > 5s                         user system elapsed plotPairwiseDEGHeatmap 7.227 0.203 8.583 createLiger 6.437 0.500 8.402 plotClusterFactorDot 4.751 0.302 5.725 plotClusterGeneViolin 4.135 0.227 5.002 plotMarkerHeatmap 4.122 0.150 5.171
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [129s/150s] OK   Running ‘testthat.R’ [128s/150s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [12s/16s] OK
• checking PDF version of manual ... [17s/20s] OK
• checking HTML version of manual ... [9s/14s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR