* using log directory ‘/data/localhost/ripley/R/packages/tests-BLIS/irlba.Rcheck’
* using R Under development (unstable) (2026-08-27 r90452)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)
    GNU Fortran (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-08-31 21:58:29 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘irlba/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘irlba’ version ‘2.3.7’
* package encoding: UTF-8
* 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 ‘irlba’ can be installed ... [6s/15s] OK
* used C compiler: ‘gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [8s/20s] OK
* checking Rd files ... 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 $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘edge.R’
  Running ‘prcomp.r’
  Running ‘ssvd.R’
  Running ‘svdr.R’
  Running ‘test.R’
 [8s/19s] ERROR
Running the tests in ‘tests/test.R’ failed.
Complete output:
  > require("irlba")
  Loading required package: irlba
  Loading required package: Matrix
  > 
  > for (FAST in c(FALSE, TRUE))
  + {
  +   # Dense matrix
  +   set.seed(1)
  +   A <- matrix(rnorm(400), 20)
  +   L <- irlba(A, nu=2, nv=2, tol=1e-9, fastpath=FAST)
  +   S <- svd(A, nu=2, nv=2)
  +   if (!isTRUE(all.equal(L$d, S$d[1:2])))
  +   {
  +     stop("Failed simple dense singular value test", " fastpath=", FAST)
  +   }
  + 
  +   # restart
  +   L1 <- irlba(A, nv=3, v=L, fastpath=FAST)
  +   if (!isTRUE(all.equal(L1$d, S$d[1:3])))
  +   {
  +     stop("Failed restart", " fastpath=", FAST)
  +   }
  + 
  +   # unequal nu, nv
  +   L <- irlba(A, nv=2, nu=3, fastpath=FAST)
  +   if (!isTRUE(ncol(L$v) == 2 && ncol(L$u) == 3))
  +   {
  +     stop("Failed unequal nu,nv", " fastpath=", FAST)
  +   }
  + 
  +   # Scaling and centering, dense
  +   s <- sqrt(apply(A, 2, crossprod))
  +   m <- colMeans(A)
  +   L <- irlba(A, 3, tol=1e-9, center=m, scale=s, fastpath=FAST)
  +   S <- svd(scale(A, center=TRUE, scale=s))
  +   if (!isTRUE(all.equal(L$d, S$d[1:3])))
  +   {
  +     stop("Failed scaling/centering test", " fastpath=", FAST)
  +   }
  +   # Scale only, non-square, dense
  +   A <- matrix(rnorm(200), 10)
  +   s <- seq(1, ncol(A))
  +   m <- colMeans(A)
  +   L <- irlba(A, 3, tol=1e-9, scale=s, fastpath=FAST)
  +   S <- svd(scale(A, center=FALSE, scale=s))
  +   if (!isTRUE(all.equal(L$d, S$d[1:3])))
  +   {
  +     stop("Failed dense scaling test", " fastpath=", FAST)
  +   }
  +   # Center only, non-square, dense
  +   L <- irlba(A, 3, tol=1e-9, center=m, fastpath=FAST)
  +   S <- svd(scale(A, center=TRUE, scale=FALSE))
  +   if (!isTRUE(all.equal(L$d, S$d[1:3])))
  +   {
  +     stop("Failed dense centering test", " fastpath=", FAST)
  +   }
  +   # Sparse matrix
  +   require("Matrix")
  +   K <- 400
  +   N <- 2000
  +   i <- sample(K, size=N, replace=TRUE)
  +   j <- sample(K, size=N, replace=TRUE)
  +   A <- sparseMatrix(i, j, x=rnorm(N))
  +   L <- irlba(A, nu=2, nv=2, tol=1e-9, fastpath=FAST)
  +   S <- svd(A, nu=2, nv=2)
  +   if (!isTRUE(all.equal(L$d, S$d[1:2])))
  +   {
  +     stop("Failed simple sparse singular value test", " fastpath=", FAST)
  +   }
  +   # Center only, sparse
  +   m <- colMeans(A)
  +   L <- irlba(A, 3, tol=1e-9, center=m, fastpath=FAST)
  +   S <- svd(scale(A, center=TRUE, scale=FALSE))
  +   if (!isTRUE(all.equal(L$d, S$d[1:3])))
  +   {
  +     stop("Failed sparse centering test", " fastpath=", FAST)
  +   }
  +   # scale only, spase
  +   s <- seq(1, ncol(A))
  +   L <- irlba(A, 3, tol=1e-9, scale=s, fastpath=FAST)
  +   S <- svd(scale(A, center=FALSE, scale=s))
  +   if (!isTRUE(all.equal(L$d, S$d[1:3])))
  +   {
  +     stop("Failed sparse scaling test", " fastpath=", FAST)
  +   }
  + 
  +   # Symmetric partial eigendecomposition
  +   set.seed(1)
  +   V <- qr.Q(qr(matrix(runif(100), nrow=10)))
  +   x <- V %*% diag(c(10, -9, 8, -7, 6, -5, 4, -3, 2, -1)) %*% t(V)
  +   if (!isTRUE(all.equal(partial_eigen(x, 3, fastpath=FAST)$values, c(10, 8, 6))))
  +   {
  +     stop("Failed partial_eigen test", " fastpath=", FAST)
  +   }
  + 
  +   # Test right-only option
  +   L <- irlba(A, 2, tol=1e-3, right_only=TRUE, fastpath=FAST, work=20)
  +   S <- svd(A, nu=2, nv=2)
  +   if (isTRUE(max(L$d - S$d[1:2]) > 1e-3))
  +   {
  +     stop("Failed right_only test", " fastpath=", FAST)
  +   }
  + 
  +   # Dense complex-valued matrix
  +   A <- matrix(rnorm(400), 20) + 1i * matrix(rnorm(400), 20)
  +   L <- irlba(A, nu=2, nv=2, tol=1e-9, fastpath=FAST)
  +   S <- svd(A, nu=2, nv=2)
  +   if (!isTRUE(all.equal(L$d, S$d[1:2])))
  +   {
  +     stop("Failed complex-valued dense singular value test", " fastpath=", FAST)
  +   }
  + 
  +   # test extra reorthogonalization
  +   L <- irlba(A, nu=2, nv=2, tol=1e-9, reorth=TRUE, fastpath=FAST)
  +   if (!isTRUE(all.equal(L$d, S$d[1:2])))
  +   {
  +     stop("Failed reorthogonalization test", " fastpath=", FAST)
  +   }
  + 
  +   # very non-square dense matrices
  +   set.seed(1)
  +   A <- matrix(rnorm(2000), 20)
  +   L1 <- irlba(A, nu=2, nv=2, tol=1e-9, fastpath=FAST)
  +   L2 <- irlba(t(A), nu=2, nv=2, tol=1e-9, fastpath=FAST)
  +   if (!isTRUE(all.equal(L1$d, L2$d)))
  +   {
  +     stop("Failed nonsquare test", " fastpath=", FAST)
  +   }
  + 
  + # This pathological example was provided by Giuseppe Rodriguez, http://bugs.unica.it/~gppe/
  + # The singular values cluster at 1 and 0, making it hard to converge to a truncated
  + # subspace containing the largest few singular values (they are all very close).
  + # Or, for that matter, the smallest.
  + #
  + #   Reference:
  + #   J. M. Varah. The Prolate matrix. Linear Algebra and Appl.,
  + #   187:269-278, 1993.
  + #  Michela Redivo-Zaglia, University of Padova, Italy
  + #       Email: Michela.RedivoZaglia@unipd.it
  + #  Giuseppe Rodriguez, University of Cagliari, Italy
  + #       Email: rodriguez@unica.it
  +   tprolate <- function(n, w=0.25)
  +   {
  +     a <- rep(0, n)
  +     a[1] <- 2 * w
  +     a[2:n] <- sin(2 * pi * w * (1:(n-1))) / (pi * (1:(n-1)))
  +     toeplitz(a)
  +   }
  + 
  +   x <- tprolate(512)
  +   set.seed(1)
  +   l <- irlba(x, nv=20, fastpath=FAST)
  +   if (isTRUE(max(abs(l$d - 1)) > 1e-3))
  +   {
  +     stop("Failed tprolate test fastpath=", FAST)
  +   }
  + 
  +   # test for issue #7 and issue #14
  +   mx <- matrix(sample(1:100, 100 * 100, replace=TRUE), nrow=100)
  +   set.seed(1)
  +   l <- irlba(mx, nv=30, center=colMeans(mx), fastpath=FAST)
  +   s <- svd(scale(mx, center=TRUE, scale=FALSE))
  +   if (isTRUE(max(abs(l$d - s$d[1:30])) > 1e-3))
  +   {
  +     stop("Failed integer matrix test fastpath=", FAST)
  +   }
  + 
  +   # test for https://github.com/bwlewis/irlba/issues/22
  +   set.seed(1000)
  +   ncells <- 50
  +   ngenes <- 1000
  +   counts <- matrix(as.double(rpois(ncells*ngenes, lambda=100)), nrow=ncells)
  +   centers <- colMeans(counts)
  +   set.seed(1)
  +   out <- irlba(scale(counts, scale=FALSE, center=centers), nu=10, nv=10)
  +   set.seed(1)
  +   l <- irlba(counts, center=centers, nu=10, nv=10, fastpath=FAST)
  +   if (isTRUE(max(abs(out$d - l$d)) > 1e-3))
  +   {
  +     stop("Failed centering test (n > m) fastpath=", FAST)
  +   }
  + 
  +   # test for https://github.com/bwlewis/irlba/issues/42
  +   set.seed(1234)
  +   a <- matrix(rnorm(10000), ncol=20)
  +   center <- runif(ncol(a))
  +   scale <- runif(ncol(a))
  +   L <- irlba(a, 5, scale=scale, center=center, fastpath=FAST)
  +   S <- svd(scale(a, center=center, scale=scale))
  +   if (isTRUE(max(abs(S$d[1:5] - L$d)) > 1e-3))
  +   {
  +     stop("Failed scale + center test fastpath=", FAST)
  +   }
  + }
  Error: Failed tprolate test fastpath=FALSE
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [8s/20s] OK
* checking PDF version of manual ... [4s/11s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/localhost/ripley/R/packages/tests-BLIS/irlba.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:46.81, 57.71 + 8.54