• 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 ‘CRMetrics/DESCRIPTION’ ... OK
• this is package ‘CRMetrics’ version ‘0.3.2’
• 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 ‘CRMetrics’ can be installed ... [7s/7s] OK See the install log 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 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 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 ... [4s/4s] 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 examples ... [4s/4s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [10s/10s] ERROR   Running ‘testthat.R’ [9s/10s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > # This file is part of the standard setup for testthat.   > # It is recommended that you do not modify it.   > #   > # Where should you do additional test configuration?   > # Learn more about the roles of various files in:   > # * https://r-pkgs.org/tests.html   > # * https://testthat.r-lib.org/reference/test_package.html#special-files   >   > library(testthat)   > library(CRMetrics)   >   > test_check("CRMetrics")      Attaching package: 'magrittr'      The following objects are masked from 'package:testthat':          equals, is_less_than, not      Adding list of 4 count matrices.   Running preprocessing using pagoda2...   3000 cells, 10000 genes; normalizing ...   Using plain model   Winsorizing ...   log scale ...   done.      calculating variance fit ...    using gam   0 overdispersed genes ... 0   persisting ...   done.   running PCA using 3000 OD genes .   .   [ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('tests.R:34:3'): Check preprocessing ─────────────────────────────────   Error in `irlba(x, nv = nPcs, nu = 0, center = cm, right_only = FALSE,       fastpath = fastpath, maxit = maxit, reorth = TRUE, ...)`: function 'as_cholmod_sparse' not provided by package 'Matrix'   Backtrace:       ▆    1. └─crm$doPreprocessing(min.transcripts.per.cell = 0, min.cells.per.gene = 0) at tests.R:34:3    2. └─base::lapply(...)    3. └─pagoda2 (local) FUN(X[[i]], ...)    4. └─p2$calculatePcaReduction(...)    5. └─irlba::irlba(...)   ── Error ('tests.R:41:3'): Check embedding object ──────────────────────────────   Error in `crm$createEmbedding(arg.embedGraph = list(method = "largeVis"))`: No preprocessed count matrices found, please run doPreprocessing.   Backtrace:       ▆    1. └─crm$createEmbedding(arg.embedGraph = list(method = "largeVis")) at tests.R:41:3      [ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ]   Error: Test failures   Execution halted
• checking PDF version of manual ... [4s/4s] OK
• DONE Status: 1 ERROR
• using check arguments '--no-clean-on-error '