* using log directory 'd:/Rcompile/CRANpkg/local/4.5/genpca.Rcheck' * using R version 4.5.3 (2026-03-11 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'genpca/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'genpca' version '0.2.1' * 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 'genpca' can be installed ... OK * used C++ compiler: 'g++.exe (GCC) 14.3.0' * 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 ... [3s] OK * checking whether the package can be loaded with stated dependencies ... [3s] OK * checking whether the package can be unloaded cleanly ... [3s] OK * checking whether the namespace can be loaded with stated dependencies ... [3s] OK * checking whether the namespace can be unloaded cleanly ... [3s] OK * checking loading without being on the library search path ... [3s] 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 ... [20s] OK * checking Rd files ... [1s] 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 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 ... [10s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [72s] ERROR Running 'testthat.R' [71s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(genpca) Registered S3 method overwritten by 'genpca': method from transfer.cross_projector multivarious Attaching package: 'genpca' The following object is masked from 'package:base': truncate > > test_check("genpca") Solving generalized eigenproblem C v = lambda R v... Preparing constraints... Applying pre-processing... Using one-shot eigen decomposition (gmdLA) to extract 1 components... gmdLA: Using primal approach (n >= p) Computing factorization for matrix R Calculating X'QX... Calculating F' X'QX F... Performing eigen decomposition on target matrix (dim: 4)... (Found 1 eigenvalues > tol) Calculating ov (V = F^{-T} * eigenvectors)... Calculating ou (U)... Calculating explained variance... Constructing final object... GPCA finished. gmdLA: Using primal approach (n >= p) Calculating X'QX... Calculating F' X'QX F... Performing eigen decomposition on target matrix (dim: 4)... (Found 1 eigenvalues > tol) Calculating ov (V = F^{-T} * eigenvectors)... Calculating ou (U)... Calculating explained variance... Deflation component 1 u norm near zero, stopping power iteration for component 1 Preparing constraints... Applying pre-processing... Deflation component 1 Preparing constraints... Applying pre-processing... Deflation component 1 Computing top-1 GPLSSVD components via operator (eigencore) ... Preparing constraints... Applying pre-processing... Calculating variance explained for Spectra method... Constructing final object... GPCA finished. Matrix M is not SPD, replacing with identity matrix Preparing constraints... Applying pre-processing... Using one-shot eigen decomposition (gmdLA) to extract 2 components... gmdLA: Using primal approach (n >= p) Computing factorization for matrix R Calculating X'QX... Calculating F' X'QX F... Performing eigen decomposition on target matrix (dim: 5)... (Found 2 eigenvalues > tol) Calculating ov (V = F^{-T} * eigenvectors)... Calculating ou (U)... Calculating explained variance... Constructing final object... Preparing constraints... Applying pre-processing... Using randomized block solver to extract 2 components (oversample=2, n_power=1, n_polish=1, tol_polish=1e-04). Calculating variance explained for randomized method... Constructing final object... GPCA finished. gmdLA: Using primal approach (n >= p) Computing factorization for matrix R Calculating X'QX... Calculating F' X'QX F... Performing eigen decomposition on target matrix (dim: 5)... (Found 2 eigenvalues > tol) Calculating ov (V = F^{-T} * eigenvectors)... Calculating ou (U)... Calculating explained variance... gmdLA: Using dual approach (n < p) Computing factorization for matrix Q Calculating X R X'... Calculating F' X R X' F... Performing eigen decomposition on target matrix (dim: 5)... (Found 2 eigenvalues > tol) Calculating ou (U = F^{-T} * eigenvectors)... Calculating ov (V = X' Q U D^{-1})... Calculating explained variance... Computing eigen factorization of R... Computing R^{1/2} C R^{1/2}... Computing eigendecomposition... Mapping back: V = R^{-1/2} Z... Solving generalized eigenproblem C v = lambda R v... Solving generalized eigenproblem C v = lambda R v... Matrix R is not SPD, replacing with identity matrix Solving generalized eigenproblem C v = lambda R v... Solving generalized eigenproblem C v = lambda R v... Matrix R is not SPD, replacing with identity matrix Solving generalized eigenproblem C v = lambda R v... Attaching package: 'multivarious' The following object is masked from 'package:testthat': pass The following objects are masked from 'package:stats': residuals, screeplot The following objects are masked from 'package:base': transform, truncate 'as(, "dgCMatrix")' is deprecated. Use 'as(as(., "generalMatrix"), "CsparseMatrix")' instead. See help("Deprecated") and help("Matrix-deprecated"). Saving _problems/test-gplssvd-op-large-99.R Extracting component 1/2 [penalty=l1, lambda=0.05] Extracting component 2/2 [penalty=l1, lambda=0.1] Extracting component 1/2 [penalty=l1, lambda=0.1] v_k => all zero, stopping. Extracting component 1/2 [penalty=l1, lambda=1e+06] v_k => all zero, stopping. sigma is 3.00269080945555 sigma is 3.40988208633537 MSE no constraint: 0.2154146 MSE adjacency: 0.2154525 [ FAIL 1 | WARN 83 | SKIP 1 | PASS 1582 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-gplssvd_op.R:4:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-gplssvd-op-large.R:99:3'): irlba backend works beyond the dense fallback threshold ── Error in `irlba::irlba(A0, nv = k, nu = k, work = max(3 * k, k + 1), tol = if (!is.null(svd_opts$tol)) svd_opts$tol else 1e-07, maxit = if (!is.null(svd_opts$maxitr)) svd_opts$maxitr else 1000, mult = mult_fun, fastpath = FALSE)`: starting vector near the null space Backtrace: ▆ 1. └─genpca::gplssvd_op(X, Y, k = k, svd_backend = "irlba") at test-gplssvd-op-large.R:99:3 2. └─irlba::irlba(...) [ FAIL 1 | WARN 83 | SKIP 1 | PASS 1582 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [55s] OK * checking PDF version of manual ... [19s] OK * checking HTML version of manual ... [10s] OK * DONE Status: 1 ERROR