Last updated on 2024-03-28 06:01:23 CET.
Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
---|---|---|---|---|---|---|
r-devel-linux-x86_64-debian-clang | 5.5.12 | 195.63 | 391.05 | 586.68 | NOTE | |
r-devel-linux-x86_64-debian-gcc | 5.5.12 | 149.54 | 298.25 | 447.79 | NOTE | |
r-devel-linux-x86_64-fedora-clang | 5.5.12 | 803.53 | NOTE | |||
r-devel-linux-x86_64-fedora-gcc | 5.5.12 | 838.90 | NOTE | |||
r-devel-windows-x86_64 | 5.5.12 | 168.00 | 244.00 | 412.00 | ERROR | |
r-patched-linux-x86_64 | 5.5.12 | 182.81 | 388.77 | 571.58 | NOTE | |
r-release-linux-x86_64 | 5.5.12 | 181.88 | 387.56 | 569.44 | NOTE | |
r-release-macos-arm64 | 5.5.12 | 212.00 | NOTE | |||
r-release-macos-x86_64 | 5.5.12 | 402.00 | NOTE | |||
r-release-windows-x86_64 | 5.5.12 | 203.00 | 376.00 | 579.00 | NOTE | |
r-oldrel-macos-arm64 | 5.5.12 | 167.00 | NOTE | |||
r-oldrel-windows-x86_64 | 5.5.12 | 195.00 | 375.00 | 570.00 | NOTE |
Version: 5.5.12
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-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-windows-x86_64
Version: 5.5.12
Check: examples
Result: ERROR
Running examples in 'dtwclust-Ex.R' failed
The error most likely occurred in:
> ### Name: compare_clusterings
> ### Title: Compare different clustering configurations
> ### Aliases: compare_clusterings
>
> ### ** Examples
>
> # Fuzzy preprocessing: calculate autocorrelation up to 50th lag
> acf_fun <- function(series, ...) {
+ lapply(series, function(x) {
+ as.numeric(acf(x, lag.max = 50, plot = FALSE)$acf)
+ })
+ }
>
> # Define overall configuration
> cfgs <- compare_clusterings_configs(
+ types = c("p", "h", "f", "t"),
+ k = 19L:20L,
+ controls = list(
+ partitional = partitional_control(
+ iter.max = 30L,
+ nrep = 1L
+ ),
+ hierarchical = hierarchical_control(
+ method = "all"
+ ),
+ fuzzy = fuzzy_control(
+ # notice the vector
+ fuzziness = c(2, 2.5),
+ iter.max = 30L
+ ),
+ tadpole = tadpole_control(
+ # notice the vectors
+ dc = c(1.5, 2),
+ window.size = 19L:20L
+ )
+ ),
+ preprocs = pdc_configs(
+ type = "preproc",
+ # shared
+ none = list(),
+ zscore = list(center = c(FALSE)),
+ # only for fuzzy
+ fuzzy = list(
+ acf_fun = list()
+ ),
+ # only for tadpole
+ tadpole = list(
+ reinterpolate = list(new.length = 205L)
+ ),
+ # specify which should consider the shared ones
+ share.config = c("p", "h")
+ ),
+ distances = pdc_configs(
+ type = "distance",
+ sbd = list(),
+ fuzzy = list(
+ L2 = list()
+ ),
+ share.config = c("p", "h")
+ ),
+ centroids = pdc_configs(
+ type = "centroid",
+ partitional = list(
+ pam = list()
+ ),
+ # special name 'default'
+ hierarchical = list(
+ default = list()
+ ),
+ fuzzy = list(
+ fcmdd = list()
+ ),
+ tadpole = list(
+ default = list(),
+ shape_extraction = list(znorm = TRUE)
+ )
+ )
+ )
>
> # Number of configurations is returned as attribute
> num_configs <- sapply(cfgs, attr, which = "num.configs")
> cat("\nTotal number of configurations without considering optimizations:",
+ sum(num_configs),
+ "\n\n")
Total number of configurations without considering optimizations: 56
>
> # Define evaluation functions based on CVI: Variation of Information (only crisp partition)
> vi_evaluators <- cvi_evaluators("VI", ground.truth = CharTrajLabels)
Some of the chosen CVIs are to be minized, but their values will be inverted by the scoring function. See this function's documentation for more details, and use suppressMessages to avoid this message.
> score_fun <- vi_evaluators$score
> pick_fun <- vi_evaluators$pick
>
> # ====================================================================================
> # Short run with only fuzzy clustering
> # ====================================================================================
>
> comparison_short <- compare_clusterings(CharTraj, types = c("f"), configs = cfgs,
+ seed = 293L, trace = TRUE,
+ score.clus = score_fun, pick.clus = pick_fun,
+ return.objects = TRUE)
=================================== Preprocessing series ===================================
-------------- Applying fuzzy preprocessings: --------------
preproc
1 acf_fun
=================================== Performing fuzzy clusterings ===================================
-------------- Using configuration: --------------
k fuzziness iter.max delta symmetric version preproc distance centroid
1 19, 20 2 30 0.001 FALSE 2 acf_fun L2 fcmdd
Precomputing distance matrix...
Flavor: r-devel-windows-x86_64
Version: 5.5.12
Check: tests
Result: ERROR
Running 'testthat.R' [57s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(dtwclust)
Loading required package: proxy
Attaching package: 'proxy'
The following objects are masked from 'package:stats':
as.dist, dist
The following object is masked from 'package:base':
as.matrix
Loading required package: dtw
Loaded dtw v1.23-1. See ?dtw for help, citation("dtw") for use in publication.
dtwclust:
Setting random number generator to L'Ecuyer-CMRG (see RNGkind()).
To read the included vignettes type: browseVignettes("dtwclust").
See news(package = "dtwclust") after package updates.
> library(foreach)
> library(testthat)
>
> # coverage for multi-threading might not be possible (?)
> if (nzchar(Sys.getenv("R_COVR"))) RcppParallel::setThreadOptions(1L)
> # old reporter for CMD checks
> options(testthat.default_reporter = "summary")
>
> #' To test in a local machine:
> #' Sys.setenv(NOT_CRAN = "true"); test_dir("tests/testthat/")
> #' OR
> #' devtools::test() # fixed? https://github.com/r-lib/devtools/issues/1832
> #'
> #' To disable parallel tests, before calling test() run:
> #'
> #' options(dtwclust_skip_par_tests = TRUE)
> #'
> testthat::test_check("dtwclust")
Flavor: r-devel-windows-x86_64
Version: 5.5.12
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'parallelization-considerations.Rmd' using rmarkdown_notangle
--- finished re-building 'parallelization-considerations.Rmd'
--- re-building 'timing-experiments.Rmd' using rmarkdown_notangle
--- finished re-building 'timing-experiments.Rmd'
--- re-building 'dtwclust.Rnw' using knitr_notangle
SUMMARY: processing the following file failed:
'dtwclust.Rnw'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 5.5.12
Check: installed package size
Result: NOTE
installed size is 9.4Mb
sub-directories of 1Mb or more:
doc 2.4Mb
libs 5.7Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64