CRAN Package Check Results for Package walker

Last updated on 2019-08-25 10:46:33 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2.5 239.88 489.19 729.07 NOTE
r-devel-linux-x86_64-debian-gcc 0.2.5 259.60 314.77 574.37 NOTE
r-devel-linux-x86_64-fedora-clang 0.2.5 960.34 WARN
r-devel-linux-x86_64-fedora-gcc 0.2.5 1046.22 NOTE
r-devel-windows-ix86+x86_64 0.2.5 362.00 618.00 980.00 NOTE
r-patched-linux-x86_64 0.2.5 246.17 465.35 711.52 NOTE
r-patched-solaris-x86 0.2.5 1840.60 NOTE
r-release-linux-x86_64 0.2.5 246.70 477.44 724.14 NOTE
r-release-windows-ix86+x86_64 0.2.5 533.00 599.00 1132.00 NOTE
r-release-osx-x86_64 0.2.5 ERROR
r-oldrel-windows-ix86+x86_64 0.2.5 498.00 701.00 1199.00 NOTE
r-oldrel-osx-x86_64 0.2.5 ERROR

Check Details

Version: 0.2.5
Check: for GNU extensions in Makefiles
Result: NOTE
    GNU make is a SystemRequirements.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.2.5
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/err/is_lower_triangular.hpp:25:27: warning: 'ptr_fun<double, double>' is deprecated [-Wdeprecated-declarations]
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.2.5
Check: installed package size
Result: NOTE
     installed size is 58.0Mb
     sub-directories of 1Mb or more:
     doc 1.8Mb
     libs 55.9Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.2.5
Check: examples
Result: ERROR
    Running examples in ‘walker-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: plot_predict
    > ### Title: Prediction intervals for walker object
    > ### Aliases: plot_predict
    >
    > ### ** Examples
    >
    > set.seed(1)
    > n <- 60
    > slope <- 0.0001 + cumsum(rnorm(n, 0, sd = 0.01))
    > beta <- numeric(n)
    > beta[1] <- 1
    > for(i in 2:n) beta[i] <- beta[i-1] + slope[i-1]
    > ts.plot(beta)
    > x <- rnorm(n, 1, 0.5)
    > alpha <- 2
    > ts.plot(beta * x)
    >
    > signal <- alpha + beta * x
    > y <- rnorm(n, signal, 0.25)
    > ts.plot(cbind(signal, y), col = 1:2)
    > data_old <- data.frame(y = y[1:(n-10)], x = x[1:(n-10)])
    > rw2_fit <- walker(y ~ 1 +
    + rw2(~ -1 + x,
    + beta_prior = c(0, 10),
    + sigma_prior = c(0, 10),
    + slope_prior = c(0, 10)),
    + sigma_y_prior = c(0, 10),
    + beta_prior = c(0, 10),
    + iter = 400, chains = 1, data = data_old)
    
    SAMPLING FOR MODEL 'walker_lm' NOW (CHAIN 1).
    Chain 1:
    Chain 1: Gradient evaluation took 0.001197 seconds
    Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 11.97 seconds.
    Chain 1: Adjust your expectations accordingly!
    Chain 1:
    Chain 1:
    Chain 1: Iteration: 1 / 400 [ 0%] (Warmup)
    [1] "Error in sampler$call_sampler(args_list[[i]]) : "
    [2] " c++ exception (unknown reason)"
    error occurred during calling the sampler; sampling not done
    >
    > pred <- predict(rw2_fit, newdata = data.frame(x=x[(n-9):n]))
    Stan model 'walker_lm' does not contain samples.
    Stan model 'walker_lm' does not contain samples.
    Error in matrix(0, n_iter, 0) : non-numeric matrix extent
    Calls: predict -> predict.walker_fit -> matrix
    Execution halted
Flavor: r-release-osx-x86_64

Version: 0.2.5
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘walker.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 124-128 (walker.Rmd)
    Error: processing vignette 'walker.Rmd' failed with diagnostics:
    argument of length 0
    --- failed re-building ‘walker.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘walker.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-osx-x86_64

Version: 0.2.5
Check: examples
Result: ERROR
    Running examples in ‘walker-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: walker
    > ### Title: Bayesian regression with random walk coefficients
    > ### Aliases: walker
    >
    > ### ** Examples
    >
    >
    > ## note very low number of iterations for the CRAN checks
    >
    > rw1_fit <- walker(Nile ~ -1 +
    + rw1(~ 1,
    + beta_prior = c(1000, 100),
    + sigma_prior = c(0, 100)),
    + sigma_y_prior = c(0, 100),
    + iter = 200, chains = 1)
    
    SAMPLING FOR MODEL 'walker_lm' NOW (CHAIN 1).
    Chain 1:
    Chain 1: Gradient evaluation took 0.001345 seconds
    Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 13.45 seconds.
    Chain 1: Adjust your expectations accordingly!
    Chain 1:
    Chain 1:
    Chain 1: WARNING: There aren't enough warmup iterations to fit the
    Chain 1: three stages of adaptation as currently configured.
    Chain 1: Reducing each adaptation stage to 15%/75%/10% of
    Chain 1: the given number of warmup iterations:
    Chain 1: init_buffer = 15
    Chain 1: adapt_window = 75
    Chain 1: term_buffer = 10
    Chain 1:
    Chain 1: Iteration: 1 / 200 [ 0%] (Warmup)
    Chain 1: Iteration: 20 / 200 [ 10%] (Warmup)
    Chain 1: Iteration: 40 / 200 [ 20%] (Warmup)
    Chain 1: Iteration: 60 / 200 [ 30%] (Warmup)
    Chain 1: Iteration: 80 / 200 [ 40%] (Warmup)
    Chain 1: Iteration: 100 / 200 [ 50%] (Warmup)
    Chain 1: Iteration: 101 / 200 [ 50%] (Sampling)
    Chain 1: Iteration: 120 / 200 [ 60%] (Sampling)
    Chain 1: Iteration: 140 / 200 [ 70%] (Sampling)
    Chain 1: Iteration: 160 / 200 [ 80%] (Sampling)
    Chain 1: Iteration: 180 / 200 [ 90%] (Sampling)
    Chain 1: Iteration: 200 / 200 [100%] (Sampling)
    Chain 1:
    Chain 1: Elapsed Time: 1.38413 seconds (Warm-up)
    Chain 1: 1.20403 seconds (Sampling)
    Chain 1: 2.58816 seconds (Total)
    Chain 1:
    Warning: The largest R-hat is 1.13, indicating chains have not mixed.
    Running the chains for more iterations may help. See
    http://mc-stan.org/misc/warnings.html#r-hat
    Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
    Running the chains for more iterations may help. See
    http://mc-stan.org/misc/warnings.html#bulk-ess
    Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
    Running the chains for more iterations may help. See
    http://mc-stan.org/misc/warnings.html#tail-ess
    >
    > rw2_fit <- walker(Nile ~ -1 +
    + rw2(~ 1,
    + beta_prior = c(1000, 100),
    + sigma_prior = c(0, 100),
    + slope_prior = c(0, 100)),
    + sigma_y_prior = c(0, 100),
    + iter = 200, chains = 1)
    
    SAMPLING FOR MODEL 'walker_lm' NOW (CHAIN 1).
    Chain 1:
    Chain 1: Gradient evaluation took 0.001423 seconds
    Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 14.23 seconds.
    Chain 1: Adjust your expectations accordingly!
    Chain 1:
    Chain 1:
    Chain 1: WARNING: There aren't enough warmup iterations to fit the
    Chain 1: three stages of adaptation as currently configured.
    Chain 1: Reducing each adaptation stage to 15%/75%/10% of
    Chain 1: the given number of warmup iterations:
    Chain 1: init_buffer = 15
    Chain 1: adapt_window = 75
    Chain 1: term_buffer = 10
    Chain 1:
    [1] "Error in sampler$call_sampler(args_list[[i]]) : "
    [2] " c++ exception (unknown reason)"
    error occurred during calling the sampler; sampling not done
    >
    > g_y <- geom_point(data = data.frame(y = Nile, x = time(Nile)),
    + aes(x, y, alpha = 0.5), inherit.aes = FALSE)
    > g_rw1 <- plot_coefs(rw1_fit) + g_y
    > g_rw2 <- plot_coefs(rw2_fit) + g_y
    Stan model 'walker_lm' does not contain samples.
    Error in 1:nrow(coef_data) : argument of length 0
    Calls: plot_coefs
    Execution halted
Flavor: r-oldrel-osx-x86_64