• using R Under development (unstable) (2026-10-05 r90641)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16.2.0-3) 16.2.0     GNU Fortran (Debian 16.2.0-3) 16.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-10-06 15:26:55 UTC
• checking for file ‘genpca/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘genpca’ version ‘0.2.1’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/3s] OK
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘genpca’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-16 (Debian 16.2.0-3) 16.2.0’
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [2s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the package can be unloaded cleanly ... [2s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
• checking loading without being on the library search path ... [2s/2s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [17s/20s] OK
• checking Rd files ... [0s/0s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [4s/4s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [35s/39s] ERROR   Running ‘testthat.R’ [35s/38s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [33s/39s] OK
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [2s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR