MADMMplasso

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examples

Running examples in ‘MADMMplasso-Ex.R’ failed
The error most likely occurred in:

> ### Name: MADMMplasso
> ### Title: MADMMplasso: Multi Variate Multi Response ADMM with Interaction
> ###   Effects
> ### Aliases: MADMMplasso-package MADMMplasso
> 
> ### ** Examples
> 
> # Train the model
> # generate some data
> set.seed(1235)
> N <- 100
> p <- 50
> nz <- 4
> K <- nz
> X <- matrix(rnorm(n = N * p), nrow = N, ncol = p)
> mx <- colMeans(X)
> sx <- sqrt(apply(X, 2, var))
> X <- scale(X, mx, sx)
> X <- matrix(as.numeric(X), N, p)
> Z <- matrix(rnorm(N * nz), N, nz)
> mz <- colMeans(Z)
> sz <- sqrt(apply(Z, 2, var))
> Z <- scale(Z, mz, sz)
> beta_1 <- rep(x = 0, times = p)
> beta_2 <- rep(x = 0, times = p)
> beta_3 <- rep(x = 0, times = p)
> beta_4 <- rep(x = 0, times = p)
> beta_5 <- rep(x = 0, times = p)
> beta_6 <- rep(x = 0, times = p)
> 
> beta_1[1:5] <- c(2, 2, 2, 2, 2)
> beta_2[1:5] <- c(2, 2, 2, 2, 2)
> beta_3[6:10] <- c(2, 2, 2, -2, -2)
> beta_4[6:10] <- c(2, 2, 2, -2, -2)
> beta_5[11:15] <- c(-2, -2, -2, -2, -2)
> beta_6[11:15] <- c(-2, -2, -2, -2, -2)
> 
> Beta <- cbind(beta_1, beta_2, beta_3, beta_4, beta_5, beta_6)
> colnames(Beta) <- 1:6
> 
> theta <- array(0, c(p, K, 6))
> theta[1, 1, 1] <- 2
> theta[3, 2, 1] <- 2
> theta[4, 3, 1] <- -2
> theta[5, 4, 1] <- -2
> theta[1, 1, 2] <- 2
> theta[3, 2, 2] <- 2
> theta[4, 3, 2] <- -2
> theta[5, 4, 2] <- -2
> theta[6, 1, 3] <- 2
> theta[8, 2, 3] <- 2
> theta[9, 3, 3] <- -2
> theta[10, 4, 3] <- -2
> theta[6, 1, 4] <- 2
> theta[8, 2, 4] <- 2
> theta[9, 3, 4] <- -2
> theta[10, 4, 4] <- -2
> theta[11, 1, 5] <- 2
> theta[13, 2, 5] <- 2
> theta[14, 3, 5] <- -2
> theta[15, 4, 5] <- -2
> theta[11, 1, 6] <- 2
> theta[13, 2, 6] <- 2
> theta[14, 3, 6] <- -2
> theta[15, 4, 6] <- -2
> 
> pliable <- matrix(0, N, 6)
> for (e in 1:6) {
+   pliable[, e] <- compute_pliable(X, Z, theta[, , e])
+ }
> 
> esd <- diag(6)
> e <- MASS::mvrnorm(N, mu = rep(0, 6), Sigma = esd)
> y_train <- X %*% Beta + pliable + e
> y <- y_train
> 
> colnames(y) <- c(paste0("y", seq_len(ncol(y))))
> TT <- tree_parms(y)
> plot(TT$h_clust)
> gg1 <- matrix(0, 2, 2)
> gg1[1, ] <- c(0.02, 0.02)
> gg1[2, ] <- c(0.02, 0.02)
> 
> nlambda <- 1
> e.abs <- 1E-4
> e.rel <- 1E-2
> alpha <- 0.2
> tol <- 1E-3
> fit <- MADMMplasso(
+   X, Z, y,
+   alpha = alpha, my_lambda = matrix(rep(0.2, ncol(y)), 1),
+   lambda_min = 0.001, max_it = 1000, e.abs = e.abs, e.rel = e.rel,
+   maxgrid = nlambda, nlambda = nlambda, rho = 5, tree = TT, my_print = FALSE,
+   alph = TRUE, gg = gg1, tol = tol, cl = 2L
+ )
Error in unserialize(socklist[[n]]) : error reading from connection
Calls: MADMMplasso ... recvOneData -> recvOneData.SOCKcluster -> unserialize
Execution halted

tests

  Running ‘testthat.R’ [8s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > testthat::test_check("MADMMplasso")
  Loading required package: MADMMplasso
  Saving _problems/test-issue_53-89.R
  Saving _problems/test-issue_62-74.R
  Saving _problems/test-parallel-86.R
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 102 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-issue_53.R:83:1'): (code run outside of `test_that()`) ─────────
  Error in `unserialize(socklist[[n]])`: error reading from connection
  Backtrace:
      ▆
   1. └─MADMMplasso::MADMMplasso(...) at test-issue_53.R:83:1
   2.   └─foreach(i = 1:nlambda) %dopar% ...
   3.     └─e$fun(obj, substitute(ex), parent.frame(), e$data)
   4.       └─parallel::clusterApplyLB(cl, argsList, evalWrapper)
   5.         └─parallel:::dynamicClusterApply(cl, fun, length(x), argfun)
   6.           └─parallel:::recvOneResult(cl)
   7.             ├─parallel::recvOneData(cl)
   8.             └─parallel:::recvOneData.SOCKcluster(cl)
   9.               └─base::unserialize(socklist[[n]])
  ── Error ('test-issue_62.R:68:1'): (code run outside of `test_that()`) ─────────
  Error in `unserialize(socklist[[n]])`: error reading from connection
  Backtrace:
      ▆
   1. └─MADMMplasso::MADMMplasso(...) at test-issue_62.R:68:1
   2.   └─foreach(i = 1:nlambda) %dopar% ...
   3.     └─e$fun(obj, substitute(ex), parent.frame(), e$data)
   4.       └─parallel::clusterApplyLB(cl, argsList, evalWrapper)
   5.         └─parallel:::dynamicClusterApply(cl, fun, length(x), argfun)
   6.           └─parallel:::recvOneResult(cl)
   7.             ├─parallel::recvOneData(cl)
   8.             └─parallel:::recvOneData.SOCKcluster(cl)
   9.               └─base::unserialize(socklist[[n]])
  ── Error ('test-parallel.R:78:3'): (code run outside of `test_that()`) ─────────
  Error in `unserialize(socklist[[n]])`: error reading from connection
  Backtrace:
       ▆
    1. └─MADMMplasso (local) mad_wrap(legacy = TRUE, cl = r_cl, pal = FALSE) at test-parallel.R:96:3
    2.   ├─base::suppressMessages(...) at test-parallel.R:78:3
    3.   │ └─base::withCallingHandlers(...)
    4.   └─MADMMplasso::MADMMplasso(...)
    5.     └─foreach(i = 1:nlambda) %dopar% ...
    6.       └─e$fun(obj, substitute(ex), parent.frame(), e$data)
    7.         └─parallel::clusterApplyLB(cl, argsList, evalWrapper)
    8.           └─parallel:::dynamicClusterApply(cl, fun, length(x), argfun)
    9.             └─parallel:::recvOneResult(cl)
   10.               ├─parallel::recvOneData(cl)
   11.               └─parallel:::recvOneData.SOCKcluster(cl)
   12.                 └─base::unserialize(socklist[[n]])
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 102 ]
  Error:
  ! Test failures.
  Warning messages:
  1: In for (i in seq_len(n)) { :
    closing unused connection 6 (<-localhost:11221)
  2: In for (i in seq_len(n)) { :
    closing unused connection 5 (<-localhost:11221)
  Execution halted

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installed package size

  installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb

installed package size

  installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb

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