* using log directory ‘/data/localhost/ripley/R/packages/tests-OpenBLAS/genpca.Rcheck’ * using R Under development (unstable) (2026-09-15 r90540) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) GNU Fortran (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-09-15 16:45:01 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘genpca/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘genpca’ version ‘0.2.0’ * 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 ‘genpca’ can be installed ... [56s/44s] OK * used C++ compiler: ‘g++ (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’ * 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... [16s/17s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... 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 use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [35s/36s] [35s/36s] ERROR 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") Saving _problems/test-coverage-95-branches-206.R 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"). 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 73 | SKIP 1 | PASS 1587 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-gplssvd_op.R:4:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-coverage-95-branches.R:206:3'): MN-PCA validation and graphical-lasso branches are covered ── Expected `genpca:::.mnpca_safe_solve_spd(matrix(NaN, 2, 2))` to throw a error. [ FAIL 1 | WARN 73 | SKIP 1 | PASS 1587 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [34s/34s] OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/localhost/ripley/R/packages/tests-OpenBLAS/genpca.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 3:08.93, 178.07 + 15.18