Last updated on 2024-12-22 10:50:31 CET.
| Package | ERROR | OK |
|---|---|---|
| CRMetrics | 1 | 12 |
Current CRAN status: ERROR: 1, OK: 12
Version: 0.3.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [9s/9s]
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
Flavor: r-oldrel-macos-arm64