CRAN Package Check Results for Maintainer ‘Bradley R. Buchsbaum <brad.buchsbaum at gmail.com>’

Last updated on 2026-10-15 05:59:02 CEST.

Package	OK	NOTE	ERROR	Other
adjoin	13
albersdown	13
bidser	13
colorplane	13
deflist	13
delarr	13
eigencore	13
fmriAR	13
fmrihrf	13
genpca	5		8
multivarious	11	2
neuroim	9	4
neuroim2	8		5
shard	13			1

Package adjoin

Current CRAN status: OK: 13

Package albersdown

Current CRAN status: OK: 13

Package bidser

Current CRAN status: OK: 13

Package colorplane

Current CRAN status: OK: 13

Package deflist

Current CRAN status: OK: 13

Package delarr

Current CRAN status: OK: 13

Package eigencore

Current CRAN status: OK: 13

Package fmriAR

Current CRAN status: OK: 13

Package fmrihrf

Current CRAN status: OK: 13

Package genpca

Current CRAN status: OK: 5, ERROR: 8

Version: 0.2.1
Check: tests
Result: ERROR Running ‘testthat.R’ [59s/75s] 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-clang

Version: 0.2.1
Check: tests
Result: ERROR Running ‘testthat.R’ [37s/48s] 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’ [35s/35s] 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' [50s] 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-windows-x86_64

Version: 0.2.1
Check: tests
Result: ERROR Running ‘testthat.R’ [56s/72s] 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’ [56s/66s] 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-release-linux-x86_64

Version: 0.2.1
Check: tests
Result: 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(<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

Package multivarious

Current CRAN status: OK: 11, NOTE: 2

Version: 0.3.2
Check: Rd contents
Result: NOTE Rd files without \usage: ‘perm_test.Rd’ \arguments should not be documented without \usage. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package neuroim

Current CRAN status: OK: 9, NOTE: 4

Version: 0.0.6
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘Bradley Buchsbaum <brad.buchsbaum@gmail.com>’ No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: c(person(given = c("Bradley", "R."), family = "Buchsbaum", role = "aut"), person(given = "Bradley", family = "Buchsbaum", role = "cre", email = "brad.buchsbaum@gmail.com")) as necessary. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.0.6
Check: compiled code
Result: NOTE File ‘neuroim/libs/neuroim.so’: Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’ It is good practice to register native routines and to disable symbol search. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Package neuroim2

Current CRAN status: OK: 8, ERROR: 5

Version: 0.19.1
Check: tests
Result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [69s/86s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(neuroim2) Loading required package: Matrix > > test_check("neuroim2") Saving _problems/test-io-conformance-420.R [ FAIL 1 | WARN 34 | SKIP 77 | PASS 7690 ] ══ Skipped tests (77) ══════════════════════════════════════════════════════════ • On CRAN (76): 'test-cgb.R:2:3', 'test-cgb.R:45:3', 'test-cgb.R:93:3', 'test-cgb.R:118:3', 'test-cgb.R:143:3', 'test-clusteredneurovol.R:5:3', 'test-clusteredneurovol.R:35:3', 'test-clusteredneurovol.R:50:3', 'test-clusteredneurovol.R:67:3', 'test-clusteredneurovol.R:87:3', 'test-clusteredneurovol.R:103:3', 'test-clusteredneurovol.R:117:3', 'test-downsample.R:5:3', 'test-downsample.R:23:3', 'test-downsample.R:63:3', 'test-downsample.R:79:3', 'test-downsample.R:106:3', 'test-downsample.R:228:3', 'test-downsample.R:245:3', 'test-downsample.R:284:3', 'test-downsample.R:299:3', 'test-downsample.R:326:3', 'test-enhance-stat-map.R:118:3', 'test-filebacked.R:44:3', 'test-filebacked.R:50:3', 'test-filebacked.R:86:3', 'test-filebacked.R:117:3', 'test-imageproc.R:5:3', 'test-imageproc.R:19:3', 'test-neurovec.R:121:3', 'test-nifti-extensions.R:146:3', 'test-nifti-roundtrip.R:110:3', 'test-nifti-roundtrip.R:124:3', 'test-oblique-regression.R:6:3', 'test-oblique-regression.R:22:3', 'test-oblique-regression.R:35:3', 'test-oblique-regression.R:45:3', 'test-oblique-regression.R:60:3', 'test-performance-guardrails.R:40:3', 'test-performance-guardrails.R:72:3', 'test-plot-engine.R:3:1', 'test-plot-overlay-colorbar-title.R:3:1', 'test-plot-registration-qc.R:3:1', 'test-plot-stat-fixes.R:3:1', 'test-plot-structure.R:3:1', 'test-resample-to.R:2:3', 'test-resample.R:8:3', 'test-resample.R:22:3', 'test-roi-series-fastpaths.R:390:3', 'test-searchlight-coverage.R:22:3', 'test-searchlight-coverage.R:30:3', 'test-searchlight-coverage.R:56:3', 'test-searchlight-coverage.R:74:3', 'test-searchlight-coverage.R:162:3', 'test-searchlight-coverage.R:170:3', 'test-searchlight-coverage.R:177:3', 'test-searchlight-parallel.R:12:3', 'test-searchlight-parallel.R:25:3', 'test-searchlight.R:20:3', 'test-searchlight.R:40:3', 'test-simulate.R:18:3', 'test-simulate.R:52:3', 'test-spatfilter.R:6:3', 'test-spatfilter.R:21:3', 'test-spatfilter.R:38:3', 'test-spatfilter.R:52:3', 'test-spatfilter.R:73:3', 'test-spatfilter.R:99:3', 'test-spatfilter.R:127:3', 'test-spatfilter.R:139:3', 'test-vignette-examples.R:12:1', 'test-vignette-neuro-vectors.R:4:3', 'test-vignette-pipelines.R:6:3', 'test-vignette-pipelines.R:27:3', 'test-vignette-pipelines.R:52:3', 'test-vignette-roi.R:6:3' • empty test (1): ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-io-conformance.R:420:3'): a file that is not an image is rejected with the reason ── `read_header(f)` threw an error with unexpected message. Expected match: "does\\s+not\\s+start with a NIfTI" Actual message: "'/home/hornik/tmp/scratch/RtmpXVgsxj/file744aad8c51f.nii' does not start\nwith a NIfTI or ANALYZE header.\n✖ The leading sizeof_hdr field is 0; it must be 348 (NIfTI-1/ANALYZE) or 540\n (NIfTI-2), in either byte order.\nℹ The file may be compressed with something other than gzip, be truncated, or\n not be an image at all." Backtrace: ▆ 1. ├─testthat::expect_error(read_header(f), "does\\s+not\\s+start with a NIfTI") at test-io-conformance.R:420:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─neuroim2::read_header(f) 7. ├─neuroim2::read_meta_info(desc, file_name) 8. └─neuroim2::read_meta_info(desc, file_name) 9. └─neuroim2:::.read_meta_info(x, file_name, read_nifti_header, NIFTIMetaInfo) 10. └─neuroim2 (local) read_func(hfile) 11. └─neuroim2:::.nifti_endian_and_version(conn, fname) 12. └─cli::cli_abort(...) 13. └─rlang::abort(...) [ FAIL 1 | WARN 34 | SKIP 77 | PASS 7690 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.19.1
Check: tests
Result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [22s/22s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(neuroim2) Loading required package: Matrix > > test_check("neuroim2") Saving _problems/test-io-conformance-420.R [ FAIL 1 | WARN 0 | SKIP 77 | PASS 7690 ] ══ Skipped tests (77) ══════════════════════════════════════════════════════════ • On CRAN (76): 'test-cgb.R:2:3', 'test-cgb.R:45:3', 'test-cgb.R:93:3', 'test-cgb.R:118:3', 'test-cgb.R:143:3', 'test-clusteredneurovol.R:5:3', 'test-clusteredneurovol.R:35:3', 'test-clusteredneurovol.R:50:3', 'test-clusteredneurovol.R:67:3', 'test-clusteredneurovol.R:87:3', 'test-clusteredneurovol.R:103:3', 'test-clusteredneurovol.R:117:3', 'test-downsample.R:5:3', 'test-downsample.R:23:3', 'test-downsample.R:63:3', 'test-downsample.R:79:3', 'test-downsample.R:106:3', 'test-downsample.R:228:3', 'test-downsample.R:245:3', 'test-downsample.R:284:3', 'test-downsample.R:299:3', 'test-downsample.R:326:3', 'test-enhance-stat-map.R:118:3', 'test-filebacked.R:44:3', 'test-filebacked.R:50:3', 'test-filebacked.R:86:3', 'test-filebacked.R:117:3', 'test-imageproc.R:5:3', 'test-imageproc.R:19:3', 'test-neurovec.R:121:3', 'test-nifti-extensions.R:146:3', 'test-nifti-roundtrip.R:110:3', 'test-nifti-roundtrip.R:124:3', 'test-oblique-regression.R:6:3', 'test-oblique-regression.R:22:3', 'test-oblique-regression.R:35:3', 'test-oblique-regression.R:45:3', 'test-oblique-regression.R:60:3', 'test-performance-guardrails.R:40:3', 'test-performance-guardrails.R:72:3', 'test-plot-engine.R:3:1', 'test-plot-overlay-colorbar-title.R:3:1', 'test-plot-registration-qc.R:3:1', 'test-plot-stat-fixes.R:3:1', 'test-plot-structure.R:3:1', 'test-resample-to.R:2:3', 'test-resample.R:8:3', 'test-resample.R:22:3', 'test-roi-series-fastpaths.R:390:3', 'test-searchlight-coverage.R:22:3', 'test-searchlight-coverage.R:30:3', 'test-searchlight-coverage.R:56:3', 'test-searchlight-coverage.R:74:3', 'test-searchlight-coverage.R:162:3', 'test-searchlight-coverage.R:170:3', 'test-searchlight-coverage.R:177:3', 'test-searchlight-parallel.R:12:3', 'test-searchlight-parallel.R:25:3', 'test-searchlight.R:20:3', 'test-searchlight.R:40:3', 'test-simulate.R:18:3', 'test-simulate.R:52:3', 'test-spatfilter.R:6:3', 'test-spatfilter.R:21:3', 'test-spatfilter.R:38:3', 'test-spatfilter.R:52:3', 'test-spatfilter.R:73:3', 'test-spatfilter.R:99:3', 'test-spatfilter.R:127:3', 'test-spatfilter.R:139:3', 'test-vignette-examples.R:12:1', 'test-vignette-neuro-vectors.R:4:3', 'test-vignette-pipelines.R:6:3', 'test-vignette-pipelines.R:27:3', 'test-vignette-pipelines.R:52:3', 'test-vignette-roi.R:6:3' • empty test (1): ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-io-conformance.R:420:3'): a file that is not an image is rejected with the reason ── `read_header(f)` threw an error with unexpected message. Expected match: "does\\s+not\\s+start with a NIfTI" Actual message: "'/Volumes/Temp/tmp/Rtmp4pcFyw/file154615c3783ee.nii' does not start with\na NIfTI or ANALYZE header.\n✖ The leading sizeof_hdr field is 0; it must be 348 (NIfTI-1/ANALYZE) or 540\n (NIfTI-2), in either byte order.\nℹ The file may be compressed with something other than gzip, be truncated, or\n not be an image at all." Backtrace: ▆ 1. ├─testthat::expect_error(read_header(f), "does\\s+not\\s+start with a NIfTI") at test-io-conformance.R:420:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─neuroim2::read_header(f) 7. ├─neuroim2::read_meta_info(desc, file_name) 8. └─neuroim2::read_meta_info(desc, file_name) 9. └─neuroim2:::.read_meta_info(x, file_name, read_nifti_header, NIFTIMetaInfo) 10. └─neuroim2 (local) read_func(hfile) 11. └─neuroim2:::.nifti_endian_and_version(conn, fname) 12. └─cli::cli_abort(...) 13. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 77 | PASS 7690 ] Error: ! Test failures. Execution halted Flavor: r-release-macos-arm64

Version: 0.19.1
Check: tests
Result: ERROR Running ‘spelling.R’ [0s/1s] Running ‘testthat.R’ [72s/204s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(neuroim2) Loading required package: Matrix > > test_check("neuroim2") Saving _problems/test-io-conformance-420.R [ FAIL 1 | WARN 0 | SKIP 77 | PASS 7690 ] ══ Skipped tests (77) ══════════════════════════════════════════════════════════ • On CRAN (76): 'test-cgb.R:2:3', 'test-cgb.R:45:3', 'test-cgb.R:93:3', 'test-cgb.R:118:3', 'test-cgb.R:143:3', 'test-clusteredneurovol.R:5:3', 'test-clusteredneurovol.R:35:3', 'test-clusteredneurovol.R:50:3', 'test-clusteredneurovol.R:67:3', 'test-clusteredneurovol.R:87:3', 'test-clusteredneurovol.R:103:3', 'test-clusteredneurovol.R:117:3', 'test-downsample.R:5:3', 'test-downsample.R:23:3', 'test-downsample.R:63:3', 'test-downsample.R:79:3', 'test-downsample.R:106:3', 'test-downsample.R:228:3', 'test-downsample.R:245:3', 'test-downsample.R:284:3', 'test-downsample.R:299:3', 'test-downsample.R:326:3', 'test-enhance-stat-map.R:118:3', 'test-filebacked.R:44:3', 'test-filebacked.R:50:3', 'test-filebacked.R:86:3', 'test-filebacked.R:117:3', 'test-imageproc.R:5:3', 'test-imageproc.R:19:3', 'test-neurovec.R:121:3', 'test-nifti-extensions.R:146:3', 'test-nifti-roundtrip.R:110:3', 'test-nifti-roundtrip.R:124:3', 'test-oblique-regression.R:6:3', 'test-oblique-regression.R:22:3', 'test-oblique-regression.R:35:3', 'test-oblique-regression.R:45:3', 'test-oblique-regression.R:60:3', 'test-performance-guardrails.R:40:3', 'test-performance-guardrails.R:72:3', 'test-plot-engine.R:3:1', 'test-plot-overlay-colorbar-title.R:3:1', 'test-plot-registration-qc.R:3:1', 'test-plot-stat-fixes.R:3:1', 'test-plot-structure.R:3:1', 'test-resample-to.R:2:3', 'test-resample.R:8:3', 'test-resample.R:22:3', 'test-roi-series-fastpaths.R:390:3', 'test-searchlight-coverage.R:22:3', 'test-searchlight-coverage.R:30:3', 'test-searchlight-coverage.R:56:3', 'test-searchlight-coverage.R:74:3', 'test-searchlight-coverage.R:162:3', 'test-searchlight-coverage.R:170:3', 'test-searchlight-coverage.R:177:3', 'test-searchlight-parallel.R:12:3', 'test-searchlight-parallel.R:25:3', 'test-searchlight.R:20:3', 'test-searchlight.R:40:3', 'test-simulate.R:18:3', 'test-simulate.R:52:3', 'test-spatfilter.R:6:3', 'test-spatfilter.R:21:3', 'test-spatfilter.R:38:3', 'test-spatfilter.R:52:3', 'test-spatfilter.R:73:3', 'test-spatfilter.R:99:3', 'test-spatfilter.R:127:3', 'test-spatfilter.R:139:3', 'test-vignette-examples.R:12:1', 'test-vignette-neuro-vectors.R:4:3', 'test-vignette-pipelines.R:6:3', 'test-vignette-pipelines.R:27:3', 'test-vignette-pipelines.R:52:3', 'test-vignette-roi.R:6:3' • empty test (1): ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-io-conformance.R:420:3'): a file that is not an image is rejected with the reason ── `read_header(f)` threw an error with unexpected message. Expected match: "does\\s+not\\s+start with a NIfTI" Actual message: "'/Volumes/Temp/tmp/RtmpyjiYsY/filed08a2f5dbacb.nii' does not start with\na NIfTI or ANALYZE header.\n✖ The leading sizeof_hdr field is 0; it must be 348 (NIfTI-1/ANALYZE) or 540\n (NIfTI-2), in either byte order.\nℹ The file may be compressed with something other than gzip, be truncated, or\n not be an image at all." Backtrace: ▆ 1. ├─testthat::expect_error(read_header(f), "does\\s+not\\s+start with a NIfTI") at test-io-conformance.R:420:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─neuroim2::read_header(f) 7. ├─neuroim2::read_meta_info(desc, file_name) 8. └─neuroim2::read_meta_info(desc, file_name) 9. └─neuroim2:::.read_meta_info(x, file_name, read_nifti_header, NIFTIMetaInfo) 10. └─neuroim2 (local) read_func(hfile) 11. └─neuroim2:::.nifti_endian_and_version(conn, fname) 12. └─cli::cli_abort(...) 13. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 77 | PASS 7690 ] Error: ! Test failures. Execution halted Flavor: r-release-macos-x86_64

Version: 0.19.1
Check: tests
Result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [26s/26s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(neuroim2) Loading required package: Matrix > > test_check("neuroim2") Saving _problems/test-io-conformance-420.R 2026-10-15 15:18:53.879 R[9633:318860] XType: Using static font registry. [ FAIL 1 | WARN 0 | SKIP 77 | PASS 7690 ] ══ Skipped tests (77) ══════════════════════════════════════════════════════════ • On CRAN (76): 'test-cgb.R:2:3', 'test-cgb.R:45:3', 'test-cgb.R:93:3', 'test-cgb.R:118:3', 'test-cgb.R:143:3', 'test-clusteredneurovol.R:5:3', 'test-clusteredneurovol.R:35:3', 'test-clusteredneurovol.R:50:3', 'test-clusteredneurovol.R:67:3', 'test-clusteredneurovol.R:87:3', 'test-clusteredneurovol.R:103:3', 'test-clusteredneurovol.R:117:3', 'test-downsample.R:5:3', 'test-downsample.R:23:3', 'test-downsample.R:63:3', 'test-downsample.R:79:3', 'test-downsample.R:106:3', 'test-downsample.R:228:3', 'test-downsample.R:245:3', 'test-downsample.R:284:3', 'test-downsample.R:299:3', 'test-downsample.R:326:3', 'test-enhance-stat-map.R:118:3', 'test-filebacked.R:44:3', 'test-filebacked.R:50:3', 'test-filebacked.R:86:3', 'test-filebacked.R:117:3', 'test-imageproc.R:5:3', 'test-imageproc.R:19:3', 'test-neurovec.R:121:3', 'test-nifti-extensions.R:146:3', 'test-nifti-roundtrip.R:110:3', 'test-nifti-roundtrip.R:124:3', 'test-oblique-regression.R:6:3', 'test-oblique-regression.R:22:3', 'test-oblique-regression.R:35:3', 'test-oblique-regression.R:45:3', 'test-oblique-regression.R:60:3', 'test-performance-guardrails.R:40:3', 'test-performance-guardrails.R:72:3', 'test-plot-engine.R:3:1', 'test-plot-overlay-colorbar-title.R:3:1', 'test-plot-registration-qc.R:3:1', 'test-plot-stat-fixes.R:3:1', 'test-plot-structure.R:3:1', 'test-resample-to.R:2:3', 'test-resample.R:8:3', 'test-resample.R:22:3', 'test-roi-series-fastpaths.R:390:3', 'test-searchlight-coverage.R:22:3', 'test-searchlight-coverage.R:30:3', 'test-searchlight-coverage.R:56:3', 'test-searchlight-coverage.R:74:3', 'test-searchlight-coverage.R:162:3', 'test-searchlight-coverage.R:170:3', 'test-searchlight-coverage.R:177:3', 'test-searchlight-parallel.R:12:3', 'test-searchlight-parallel.R:25:3', 'test-searchlight.R:20:3', 'test-searchlight.R:40:3', 'test-simulate.R:18:3', 'test-simulate.R:52:3', 'test-spatfilter.R:6:3', 'test-spatfilter.R:21:3', 'test-spatfilter.R:38:3', 'test-spatfilter.R:52:3', 'test-spatfilter.R:73:3', 'test-spatfilter.R:99:3', 'test-spatfilter.R:127:3', 'test-spatfilter.R:139:3', 'test-vignette-examples.R:12:1', 'test-vignette-neuro-vectors.R:4:3', 'test-vignette-pipelines.R:6:3', 'test-vignette-pipelines.R:27:3', 'test-vignette-pipelines.R:52:3', 'test-vignette-roi.R:6:3' • empty test (1): ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-io-conformance.R:420:3'): a file that is not an image is rejected with the reason ── `read_header(f)` threw an error with unexpected message. Expected match: "does\\s+not\\s+start with a NIfTI" Actual message: "'/Volumes/Temp/tmp/Rtmpk0JoeG/file25a173e7185a.nii' does not start with\na NIfTI or ANALYZE header.\n✖ The leading sizeof_hdr field is 0; it must be 348 (NIfTI-1/ANALYZE) or 540\n (NIfTI-2), in either byte order.\nℹ The file may be compressed with something other than gzip, be truncated, or\n not be an image at all." Backtrace: ▆ 1. ├─testthat::expect_error(read_header(f), "does\\s+not\\s+start with a NIfTI") at test-io-conformance.R:420:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─neuroim2::read_header(f) 7. ├─neuroim2::read_meta_info(desc, file_name) 8. └─neuroim2::read_meta_info(desc, file_name) 9. └─neuroim2:::.read_meta_info(x, file_name, read_nifti_header, NIFTIMetaInfo) 10. └─neuroim2 (local) read_func(hfile) 11. └─neuroim2:::.nifti_endian_and_version(conn, fname) 12. └─cli::cli_abort(...) 13. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 77 | PASS 7690 ] Error: ! Test failures. Execution halted Flavor: r-oldrel-macos-arm64

Version: 0.19.1
Check: tests
Result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [70s/108s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(neuroim2) Loading required package: Matrix > > test_check("neuroim2") Saving _problems/test-io-conformance-420.R [ FAIL 1 | WARN 0 | SKIP 77 | PASS 7690 ] ══ Skipped tests (77) ══════════════════════════════════════════════════════════ • On CRAN (76): 'test-cgb.R:2:3', 'test-cgb.R:45:3', 'test-cgb.R:93:3', 'test-cgb.R:118:3', 'test-cgb.R:143:3', 'test-clusteredneurovol.R:5:3', 'test-clusteredneurovol.R:35:3', 'test-clusteredneurovol.R:50:3', 'test-clusteredneurovol.R:67:3', 'test-clusteredneurovol.R:87:3', 'test-clusteredneurovol.R:103:3', 'test-clusteredneurovol.R:117:3', 'test-downsample.R:5:3', 'test-downsample.R:23:3', 'test-downsample.R:63:3', 'test-downsample.R:79:3', 'test-downsample.R:106:3', 'test-downsample.R:228:3', 'test-downsample.R:245:3', 'test-downsample.R:284:3', 'test-downsample.R:299:3', 'test-downsample.R:326:3', 'test-enhance-stat-map.R:118:3', 'test-filebacked.R:44:3', 'test-filebacked.R:50:3', 'test-filebacked.R:86:3', 'test-filebacked.R:117:3', 'test-imageproc.R:5:3', 'test-imageproc.R:19:3', 'test-neurovec.R:121:3', 'test-nifti-extensions.R:146:3', 'test-nifti-roundtrip.R:110:3', 'test-nifti-roundtrip.R:124:3', 'test-oblique-regression.R:6:3', 'test-oblique-regression.R:22:3', 'test-oblique-regression.R:35:3', 'test-oblique-regression.R:45:3', 'test-oblique-regression.R:60:3', 'test-performance-guardrails.R:40:3', 'test-performance-guardrails.R:72:3', 'test-plot-engine.R:3:1', 'test-plot-overlay-colorbar-title.R:3:1', 'test-plot-registration-qc.R:3:1', 'test-plot-stat-fixes.R:3:1', 'test-plot-structure.R:3:1', 'test-resample-to.R:2:3', 'test-resample.R:8:3', 'test-resample.R:22:3', 'test-roi-series-fastpaths.R:390:3', 'test-searchlight-coverage.R:22:3', 'test-searchlight-coverage.R:30:3', 'test-searchlight-coverage.R:56:3', 'test-searchlight-coverage.R:74:3', 'test-searchlight-coverage.R:162:3', 'test-searchlight-coverage.R:170:3', 'test-searchlight-coverage.R:177:3', 'test-searchlight-parallel.R:12:3', 'test-searchlight-parallel.R:25:3', 'test-searchlight.R:20:3', 'test-searchlight.R:40:3', 'test-simulate.R:18:3', 'test-simulate.R:52:3', 'test-spatfilter.R:6:3', 'test-spatfilter.R:21:3', 'test-spatfilter.R:38:3', 'test-spatfilter.R:52:3', 'test-spatfilter.R:73:3', 'test-spatfilter.R:99:3', 'test-spatfilter.R:127:3', 'test-spatfilter.R:139:3', 'test-vignette-examples.R:12:1', 'test-vignette-neuro-vectors.R:4:3', 'test-vignette-pipelines.R:6:3', 'test-vignette-pipelines.R:27:3', 'test-vignette-pipelines.R:52:3', 'test-vignette-roi.R:6:3' • empty test (1): ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-io-conformance.R:420:3'): a file that is not an image is rejected with the reason ── `read_header(f)` threw an error with unexpected message. Expected match: "does\\s+not\\s+start with a NIfTI" Actual message: "'/Volumes/Temp/tmp/RtmpEk02rr/file136c11509b34b.nii' does not start with\na NIfTI or ANALYZE header.\n✖ The leading sizeof_hdr field is 0; it must be 348 (NIfTI-1/ANALYZE) or 540\n (NIfTI-2), in either byte order.\nℹ The file may be compressed with something other than gzip, be truncated, or\n not be an image at all." Backtrace: ▆ 1. ├─testthat::expect_error(read_header(f), "does\\s+not\\s+start with a NIfTI") at test-io-conformance.R:420:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─neuroim2::read_header(f) 7. ├─neuroim2::read_meta_info(desc, file_name) 8. └─neuroim2::read_meta_info(desc, file_name) 9. └─neuroim2:::.read_meta_info(x, file_name, read_nifti_header, NIFTIMetaInfo) 10. └─neuroim2 (local) read_func(hfile) 11. └─neuroim2:::.nifti_endian_and_version(conn, fname) 12. └─cli::cli_abort(...) 13. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 77 | PASS 7690 ] Error: ! Test failures. Execution halted Flavor: r-oldrel-macos-x86_64

Package shard

Current CRAN status: OK: 13, Other: 1

Additional issues

donttest