CRAN Package Check Results for Package genpca

Last updated on 2026-10-08 23:52:51 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	0.2.1	63.28	215.66	278.94	OK
r-devel-linux-x86_64-debian-gcc	0.2.1	50.03	150.55	200.58	ERROR
r-devel-linux-x86_64-fedora-clang	0.2.1	47.00	139.75	186.75	ERROR
r-devel-linux-x86_64-fedora-gcc	0.2.1	63.00	147.40	210.40	ERROR
r-devel-windows-x86_64	0.2.1	85.00	294.00	379.00	OK
r-patched-linux-x86_64	0.2.1	67.62	195.71	263.33	ERROR
r-release-linux-x86_64	0.2.1				OK
r-release-macos-arm64	0.2.1	14.00	48.00	62.00	OK
r-release-macos-x86_64	0.2.1	46.00	262.00	308.00	OK
r-release-windows-x86_64	0.2.1	86.00	213.00	299.00	OK
r-oldrel-macos-arm64	0.2.1	13.00	56.00	69.00	OK
r-oldrel-macos-x86_64	0.2.1	44.00	224.00	268.00	OK
r-oldrel-windows-x86_64	0.2.1	100.00	283.00	383.00	ERROR

Check Details

Version: 0.2.1
Check: tests
Result: ERROR Running ‘testthat.R’ [37s/51s] 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(<ddiMatrix>, "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 Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.2.1
Check: tests
Result: ERROR Running ‘testthat.R’ [36s/37s] 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(<ddiMatrix>, "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 Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.2.1
Check: tests
Result: ERROR Running ‘testthat.R’ [37s/58s] 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(<ddiMatrix>, "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 73 | 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 73 | SKIP 1 | PASS 1582 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.2.1
Check: tests
Result: ERROR Running ‘testthat.R’ [56s/67s] 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(<ddiMatrix>, "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 Flavor: r-patched-linux-x86_64

Version: 0.2.1
Check: tests
Result: ERROR Running 'testthat.R' [70s] 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(<ddiMatrix>, "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 Flavor: r-oldrel-windows-x86_64