* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/SCPME.Rcheck’
* using R Under development (unstable) (2022-04-26 r82260)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘SCPME/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SCPME’ version ‘1.0’
* 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 ‘SCPME’ can be installed ... [124s/271s] OK
* 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 R 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 ... [14s/34s] 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 LazyData ... NOTE
  'LazyData' is specified without a 'data' directory
* 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 $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [6s/16s]
 [6s/17s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(SCPME)
  Loading required package: Rcpp
  Loading required package: RcppProgress
  Loading required package: doParallel
  Loading required package: foreach
  Loading required package: iterators
  Loading required package: parallel
  > 
  > test_check("SCPME")
   ----------- FAILURE REPORT -------------- 
   --- failure: length > 1 in coercion to logical ---
   --- srcref --- 
  : 
   --- package (from environment) --- 
  SCPME
   --- call from context --- 
  shrink(data$X, data$Y, path = TRUE, trace = "none")
   --- call from argument --- 
  !path || (crit.cv == "MSE")
   --- R stacktrace ---
  where 1: shrink(data$X, data$Y, path = TRUE, trace = "none")
  where 2: eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  where 3: withCallingHandlers({
      code
      NULL
  }, error = function(cnd) {
      if (can_entrace(cnd)) {
          cnd <- cnd_entrace(cnd)
      }
      return_from(env, cnd)
  })
  where 4: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)), 
      ...)
  where 5: quasi_capture(enquo(object), label, capture_error, entrace = TRUE)
  where 6 at testSCPME.R#30: expect_error(shrink(data$X, data$Y, path = TRUE, trace = "none"), 
      NA)
  where 7: eval(code, test_env)
  where 8: eval(code, test_env)
  where 9: withCallingHandlers({
      eval(code, test_env)
      if (!handled && !is.null(test)) {
          skip_empty()
      }
  }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
      message = handle_message, error = handle_error)
  where 10: doTryCatch(return(expr), name, parentenv, handler)
  where 11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  where 12: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  where 13: doTryCatch(return(expr), name, parentenv, handler)
  where 14: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), 
      names[nh], parentenv, handlers[[nh]])
  where 15: tryCatchList(expr, classes, parentenv, handlers)
  where 16: tryCatch(withCallingHandlers({
      eval(code, test_env)
      if (!handled && !is.null(test)) {
          skip_empty()
      }
  }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
      message = handle_message, error = handle_error), error = handle_fatal, 
      skip = function(e) {
      })
  where 17: test_code(NULL, exprs, env)
  where 18: source_file(path, child_env(env), wrap = wrap)
  where 19: FUN(X[[i]], ...)
  where 20: lapply(test_paths, test_one_file, env = env, wrap = wrap)
  where 21: doTryCatch(return(expr), name, parentenv, handler)
  where 22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  where 23: tryCatchList(expr, classes, parentenv, handlers)
  where 24: tryCatch(code, testthat_abort_reporter = function(cnd) {
      cat(conditionMessage(cnd), "\n")
      NULL
  })
  where 25: with_reporter(reporters$multi, lapply(test_paths, test_one_file, 
      env = env, wrap = wrap))
  where 26: test_files(test_dir = test_dir, test_package = test_package, 
      test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 
      env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 
      wrap = wrap, load_package = load_package)
  where 27: test_files(test_dir = path, test_paths = test_paths, test_package = package, 
      reporter = reporter, load_helpers = load_helpers, env = env, 
      stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 
      wrap = wrap, load_package = load_package, parallel = parallel)
  where 28: test_dir("testthat", package = package, reporter = reporter, 
      ..., load_package = "installed")
  where 29: test_check("SCPME")
  
   --- value of length: 5 type: logical ---
  [1]  TRUE FALSE FALSE FALSE FALSE
   --- function from context --- 
  function (X = NULL, Y = NULL, S = NULL, A = diag(ncol(S)), B = diag(ncol(S)), 
      C = matrix(0, ncol = ncol(B), nrow = ncol(A)), nlam = 10, 
      lam.max = NULL, lam.min.ratio = 0.001, lam = NULL, alpha = 1, 
      path = FALSE, rho = 2, mu = 10, tau.rho = 2, iter.rho = 10, 
      crit = c("ADMM", "loglik"), tol.abs = 1e-04, tol.rel = 1e-04, 
      maxit = 10000, adjmaxit = NULL, K = 5, crit.cv = c("MSE", 
          "loglik", "penloglik", "AIC", "BIC"), start = c("warm", 
          "cold"), cores = 1, trace = c("progress", "print", "none")) 
  {
      if (is.null(X) && is.null(S)) {
          stop("Must provide entry for X or S!")
      }
      if (!all(lam > 0)) {
          stop("lam must be positive!")
      }
      if (!(all(c(rho, mu, tau.rho, iter.rho, tol.abs, tol.rel, 
          maxit, adjmaxit, K, cores) > 0))) {
          stop("Entry must be positive!")
      }
      if ((alpha < 0) || (alpha > 1)) {
          stop("Alpha must be between 0 and 1!")
      }
      if (!(all(sapply(c(rho, mu, tau.rho, iter.rho, tol.abs, tol.rel, 
          maxit, adjmaxit, K, cores, nlam, lam.min.ratio, alpha), 
          length) <= 1))) {
          stop("Entry must be single value!")
      }
      if (all(c(maxit, adjmaxit, K, cores)%%1 != 0)) {
          stop("Entry must be an integer!")
      }
      if (cores < 1) {
          stop("Number of cores must be positive!")
      }
      if (((length(lam) > 1) & (!path || (crit.cv == "MSE"))) & 
          (is.null(X) || is.null(Y))) {
          stop("Must provide entry for X and Y!")
      }
      if (is.null(Y) && (crit.cv == "MSE")) {
          cat("Matrix Y not detected... will use loglik for crit.cv instead!\n\n")
          crit.cv = "loglik"
      }
      if (cores > 1 && path) {
          cat("Parallelization not possible when producing solution path. Setting cores = 1...\n\n")
          cores = 1
      }
      if (path) {
          if (match.arg(crit.cv) == "MSE") {
              cat("MSE crit.cv not available when path == TRUE... setting crit.cv == loglik\n\n")
              crit.cv = "loglik"
          }
          K = 1
      }
      if (cores > K) {
          cat("Number of cores exceeds K... setting cores = K\n\n")
          cores = K
      }
      if (is.null(adjmaxit)) {
          adjmaxit = maxit
      }
      crit = match.arg(crit)
      crit.cv = match.arg(crit.cv)
      start = match.arg(start)
      trace = match.arg(trace)
      call = match.call()
      MIN.error = AVG.error = CV.error = NULL
      n = ifelse(is.null(X), nrow(S), nrow(X))
      if (is.null(Y)) {
          Y = matrix(0)
      }
      if (is.null(S)) {
          S = (nrow(X) - 1)/nrow(X) * cov(X)
          if (nrow(A) == 0) {
              A = diag(ncol(S))
          }
          if (nrow(B) == 0) {
              B = diag(ncol(S))
          }
          if (nrow(C) == 0) {
              C = matrix(0, ncol = ncol(B), nrow = ncol(A))
          }
      }
      tau = max(eigen(crossprod(A))$values) * max(eigen(tcrossprod(B))$values) + 
          1e-08
      if (ncol(A) != ncol(S)) {
          stop("Matrix A has incompatible number of columns!")
      }
      if (nrow(B) != ncol(S)) {
          stop("Matrix B has incompatible number of rows!")
      }
      if ((nrow(C) != nrow(A)) || (ncol(C) != ncol(B))) {
          stop("Matrix C has incompatible dimensions!")
      }
      if (is.null(lam)) {
          if (!((lam.min.ratio <= 1) && (lam.min.ratio > 0))) {
              cat("lam.min.ratio must be in (0, 1]... setting to 1e-2!\n\n")
              lam.min.ratio = 0.01
          }
          if (!((nlam > 0) && (nlam%%1 == 0))) {
              cat("nlam must be a positive integer... setting to 10!\n\n")
              nlam = 10
          }
          if (is.null(lam.max)) {
              lam.max = max(abs(S - diag(S)))
          }
          lam.min = lam.min.ratio * lam.max
          lam = 10^seq(log10(lam.min), log10(lam.max), length = nlam)
      }
      else {
          lam = sort(lam)
      }
      initOmega = diag(diag(S)^(-1))
      init = A %*% initOmega %*% B - C
      zeros = matrix(0, nrow = nrow(C), ncol = ncol(C))
      if ((length(lam) > 1) && (!is.null(X) || path)) {
          if (cores > 1) {
              ADMM = CVP_ADMM(X = X, Y = Y, A = A, B = B, C = C, 
                  lam = lam, alpha = alpha, tau = tau, rho = rho, 
                  mu = mu, tau.rho = tau.rho, iter.rho = iter.rho, 
                  crit = crit, tol.abs = tol.abs, tol.rel = tol.rel, 
                  maxit = maxit, adjmaxit = adjmaxit, K = K, crit.cv = crit.cv, 
                  start = start, cores = cores, trace = trace)
              MIN.error = ADMM$min.error
              AVG.error = ADMM$avg.error
              CV.error = ADMM$cv.error
          }
          else {
              if (is.null(X)) {
                  X = matrix(0)
              }
              ADMM = CV_ADMMc(X = X, S = S, Y = Y, A = A, B = B, 
                  C = C, lam = lam, alpha = alpha, path = path, 
                  tau = tau, rho = rho, mu = mu, tau_rho = tau.rho, 
                  iter_rho = iter.rho, crit = crit, tol_abs = tol.abs, 
                  tol_rel = tol.rel, maxit = maxit, adjmaxit = adjmaxit, 
                  K = K, crit_cv = crit.cv, start = start, trace = trace)
              MIN.error = ADMM$min.error
              AVG.error = ADMM$avg.error
              CV.error = ADMM$cv.error
              Path = ADMM$path
          }
          if (((ADMM$lam == lam[1]) || ADMM$lam == lam[length(lam)]) && 
              ((length(lam) != 1) && (!path))) {
              cat("\nOptimal tuning parameter on boundary...!\n")
          }
          ADMM = ADMMc(S = S, A = A, B = B, C = C, initOmega = initOmega, 
              initZ = init, initY = zeros, lam = ADMM$lam, alpha = alpha, 
              tau = tau, rho = rho, mu = mu, tau_rho = tau.rho, 
              iter_rho = iter.rho, crit = crit, tol_abs = tol.abs, 
              tol_rel = tol.rel, maxit = maxit)
      }
      else {
          if (length(lam) > 1) {
              stop("Must set specify X, set path = TRUE, or provide single value for lam.")
          }
          ADMM = ADMMc(S = S, A = A, B = B, C = C, initOmega = initOmega, 
              initZ = init, initY = zeros, lam = lam, alpha = alpha, 
              tau = tau, rho = rho, mu = mu, tau_rho = tau.rho, 
              iter_rho = iter.rho, crit = crit, tol_abs = tol.abs, 
              tol_rel = tol.rel, maxit = maxit)
      }
      loglik = (-n/2) * (sum(ADMM$Omega * S) - determinant(ADMM$Omega, 
          logarithm = TRUE)$modulus[1] + ADMM$lam * ((1 - alpha)/2 * 
          sum((A %*% ADMM$Omega %*% B - C)^2) + alpha * sum(abs(A %*% 
          ADMM$Omega %*% B - C))))
      tuning = matrix(c(log10(ADMM$lam), ADMM$lam), ncol = 2)
      colnames(tuning) = c("log10(lam)", "lam")
      if (!path) {
          Path = NULL
      }
      returns = list(Call = call, Iterations = ADMM$Iterations, 
          Tuning = tuning, Lambdas = lam, maxit = maxit, Omega = ADMM$Omega, 
          Sigma = qr.solve(ADMM$Omega), Path = Path, Z = ADMM$Z, 
          Y = ADMM$Y, rho = ADMM$rho, Loglik = loglik, MIN.error = MIN.error, 
          AVG.error = AVG.error, CV.error = CV.error)
      class(returns) = "shrink"
      return(returns)
  }
  <bytecode: 0x4073c48>
  <environment: namespace:SCPME>
   --- function search by body ---
  Function shrink in namespace SCPME has this body.
   ----------- END OF FAILURE REPORT -------------- 
  Fatal error: length > 1 in coercion to logical
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [22s/58s] OK
* checking PDF 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, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/SCPME.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 8:58.67, 206.77 + 20.05