Check results for 'conos'

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 ‘conos/DESCRIPTION’ ... OK
this is package ‘conos’ version ‘1.5.2’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... NOTE Packages suggested but not available for checking: 'conosPanel', 'p2data'
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 ‘conos’ can be installed ... [50s/59s] 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 11.4Mb sub-directories of 1Mb or more: libs 9.6Mb
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 ... [6s/6s] 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 $(LAPACK_LIBS) ... OK
checking use of PKG_*FLAGS in Makefiles ... OK
checking compiled code ... OK
checking examples ... [2s/2s] ERROR Running examples in ‘conos-Ex.R’ failed The error most likely occurred in: > ### Name: Conos > ### Title: Conos R6 class > ### Aliases: Conos > > ### ** Examples > > > ## ------------------------------------------------ > ## Method `Conos$new` > ## ------------------------------------------------ > > con <- Conos$new(small_panel.preprocessed, n.cores=1) > > > ## ------------------------------------------------ > ## Method `Conos$buildGraph` > ## ------------------------------------------------ > > con <- Conos$new(small_panel.preprocessed, n.cores=1) > con$buildGraph(k=10, k.self=5, space='PCA', ncomps=10, n.odgenes=20, matching.method='mNN', + metric='angular', score.component.variance=TRUE, verbose=TRUE) found 0 out of 1 cached PCA space pairs ... running 1 additional PCA space pairs Error in irlba::irlba(x, nv = ncomps, nu = 0, center = cm, right_only = FALSE, : function 'as_cholmod_sparse' not provided by package 'Matrix' Calls: <Anonymous> ... FUN -> quickPlainPCA -> lapply -> FUN -> <Anonymous> Execution halted
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [2s/2s] ERROR Running ‘testthat.R’ [2s/2s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(conos) Loading required package: Matrix Loading required package: igraph Attaching package: 'igraph' The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union > > testthat::test_check("conos") Attaching package: 'testthat' The following object is masked from 'package:igraph': compare [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_functions.R:15:1'): (code run outside of `test_that()`) ──────── Error in `irlba::irlba(x, nv = ncomps, nu = 0, center = cm, right_only = FALSE, reorth = TRUE)`: function 'as_cholmod_sparse' not provided by package 'Matrix' Backtrace: ▆ 1. ├─base::suppressWarnings(con$buildGraph(ncomps = 25)) at test_functions.R:15:1 2. │ └─base::withCallingHandlers(...) 3. └─con$buildGraph(ncomps = 25) 4. └─private$updatePairs(...) 5. └─sccore::plapply(...) 6. └─base::lapply(...) 7. └─conos (local) FUN(X[[i]], ...) 8. └─conos:::quickPlainPCA(...) 9. └─base::lapply(...) 10. └─conos (local) FUN(X[[i]], ...) 11. └─irlba::irlba(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ] Error: Test failures Execution halted
checking PDF version of manual ... [4s/4s] OK
DONE Status: 2 ERRORs, 2 NOTEs
using check arguments '--no-clean-on-error '