Last updated on 2026-10-13 01:53:26 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 | 6 | 7 | ||
| multivarious | 11 | 2 | ||
| neuroim | 9 | 4 | ||
| neuroim2 | 9 | 4 | ||
| shard | 13 | 1 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 6, ERROR: 7
Version: 0.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [59s/77s]
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’ [36s/49s]
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’ [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’ [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' [69s]
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
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
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
Current CRAN status: OK: 9, ERROR: 4
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/RtmpH3mcl2/file20b855a9ca61.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’ [71s/180s]
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/RtmpvXnmy1/file905148ba0801.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
2026-10-13 11:06:09.130 R[3300:308191] 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/RtmpZlppTH/filece429efe308.nii' does not start with a\nNIfTI 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’ [69s/101s]
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/RtmpsLxJ7g/filee4c02a170cc7.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
Current CRAN status: OK: 13, Other: 1