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

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

Last updated on 2026-10-06 05:55:06 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	11		2
multivarious	11	2
neuroim	9	4
neuroim2	11	2
shard	13			1

Package adjoin

Current CRAN status: OK: 13

Package bidser

Current CRAN status: OK: 13

Package deflist

Current CRAN status: OK: 13

Package delarr

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: 11, ERROR: 2

Version: 0.2.1
Check: tests
Result: ERROR Running ‘testthat.R’ [42s/93s] 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’ [38s/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 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

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: 11, NOTE: 2

Version: 0.13.0
Check: Rd contents
Result: NOTE Rd files without \usage: ‘as-ClusteredNeuroVol-DenseNeuroVol.Rd’ ‘as.raster.Rd’ ‘image.Rd’ \arguments should not be documented without \usage. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package shard

Current CRAN status: OK: 13, Other: 1

Additional issues

donttest