- using R version 4.3.3 (2024-02-29)
- using platform: aarch64-apple-darwin20 (64-bit)
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
- running under: macOS Ventura 13.4
- using session charset: UTF-8
- checking for file ‘scDHA/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘scDHA’ version ‘1.2.2’
- 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 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 ‘scDHA’ can be installed ... [17s/23s] OK
See the install log for details.
- used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
- used SDK: ‘MacOSX11.3.sdk’
- checking installed package size ... NOTE
installed size is 7.4Mb
sub-directories of 1Mb or more:
data 4.1Mb
libs 3.0Mb
- 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 R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [2s/2s] OK
- checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
- checking whether the package can be unloaded cleanly ... [2s/2s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
- checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
- checking loading without being on the library search path ... [2s/2s] OK
- checking startup messages can be suppressed ... [2s/2s] 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 ... [6s/7s] OK
- checking Rd files ... [0s/0s] 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 ... [1s/1s] 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 compiled code ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [2s/2s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [3s/3s] ERROR
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(scDHA)
libtorch is not installed. Use `torch::install_torch()` to download and install libtorch
>
> on_cran <- function() !identical(Sys.getenv("NOT_CRAN"), "true")
>
> if((!torch::torch_is_installed()) &
+ (tolower(Sys.info()[["sysname"]]) != "windows") &
+ (!on_cran()))
+ {
+ torch::install_torch()
+ }
>
> Sys.setenv(IN_TEST_scDHA="true")
>
> test_check("scDHA")
[ FAIL 1 | WARN 0 | SKIP 2 | PASS 3 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-scDHA.R:3:3', 'test-scDHA.R:41:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-scDHA.R:21:3'): scDHA.vis can run ──────────────────────────────
Error in `irlba::irlba(L, nv = n, nu = 0, maxit = iters)`: function 'as_cholmod_sparse' not provided by package 'Matrix'
Backtrace:
▆
1. └─scDHA::scDHA.vis(result, ncores = 2, seed = 1) at test-scDHA.R:21:3
2. └─uwot::umap(data, n_threads = ncores)
3. └─uwot:::uwot(...)
4. └─uwot:::spectral_init(V, ndim = n_components, verbose = verbose)
5. └─uwot:::irlba_tsvd_normalized_laplacian_init(A, ndim, verbose = FALSE)
6. └─uwot:::irlba_spectral_tsvd(L, ndim + 1)
7. ├─base::suppressWarnings(...)
8. │ └─base::withCallingHandlers(...)
9. └─irlba::irlba(L, nv = n, nu = 0, maxit = iters)
[ FAIL 1 | WARN 0 | SKIP 2 | PASS 3 ]
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking re-building of vignette outputs ... [6s/6s] OK
- checking PDF version of manual ... [4s/4s] OK
- DONE
Status: 1 ERROR, 1 NOTE
- using check arguments '--no-clean-on-error '