- using R Under development (unstable) (2025-08-09 r88550 ucrt)
- using platform: x86_64-w64-mingw32
- R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
- running under: Windows Server 2022 x64 (build 20348)
- 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 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 whether package 'rliger' can be installed ... OK
See the install log for details.
- used C++ compiler: 'g++.exe (GCC) 14.2.0'
- 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 ... [8s] OK
- checking whether the package can be loaded with stated dependencies ... [7s] OK
- checking whether the package can be unloaded cleanly ... [8s] OK
- checking whether the namespace can be loaded with stated dependencies ... [8s] OK
- checking whether the namespace can be unloaded cleanly ... [8s] OK
- checking loading without being on the library search path ... [7s] OK
- checking whether startup messages can be suppressed ... [7s] 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 ... [39s] OK
- checking Rd files ... [3s] 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 ... [8s] 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 pragmas in C/C++ headers and code ... OK
- checking compiled code ... OK
- checking installed files from 'inst/doc' ... OK
- checking files in 'vignettes' ... OK
- checking examples ... [107s] ERROR
Running examples in 'rliger-Ex.R' failed
The error most likely occurred in:
> ### 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
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [124s] OK
Running 'testthat.R' [124s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [9s] OK
- checking PDF version of manual ... [38s] OK
- checking HTML version of manual ... [28s] OK
- DONE
Status: 1 ERROR