Last updated on 2025-02-23 15:49:53 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.0 | 155.02 | 541.70 | 696.72 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.2.0 | 110.97 | 342.54 | 453.51 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.2.0 | 712.55 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.0 | 779.76 | ERROR | |||
| r-devel-macos-arm64 | 1.2.0 | 304.00 | OK | |||
| r-devel-macos-x86_64 | 1.2.0 | 615.00 | ERROR | |||
| r-devel-windows-x86_64 | 1.2.0 | 161.00 | 580.00 | 741.00 | NOTE | |
| r-patched-linux-x86_64 | 1.2.0 | 175.25 | 491.09 | 666.34 | OK | |
| r-release-linux-x86_64 | 1.2.0 | 156.04 | 495.23 | 651.27 | OK | |
| r-release-macos-arm64 | 1.2.0 | 289.00 | NOTE | |||
| r-release-macos-x86_64 | 1.2.0 | 427.00 | NOTE | |||
| r-release-windows-x86_64 | 1.2.0 | 163.00 | 540.00 | 703.00 | NOTE | |
| r-oldrel-macos-arm64 | 1.2.0 | 347.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.2.0 | 585.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.2.0 | 197.00 | 688.00 | 885.00 | NOTE |
Version: 1.2.0
Check: DESCRIPTION meta-information
Result: NOTE
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘ZIPLN.R’
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-macos-x86_64, r-devel-windows-x86_64
Version: 1.2.0
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
Networkfamily.Rd: ggplot
PLNLDAfit.Rd: ggplot
PLNPCAfamily.Rd: ggplot2
PLNPCAfit.Rd: ggplot
PLNfamily.Rd: ggplot2
PLNmixturefamily.Rd: ggplot2, ggplot
PLNmixturefit.Rd: ggplot
plot.PLNLDAfit.Rd: ggplot2
plot.PLNPCAfit.Rd: ggplot
plot.PLNmixturefit.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Version: 1.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [8s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(PLNmodels)
This is packages 'PLNmodels' version 1.2.0
Use future::plan(multicore/multisession) to speed up PLNPCA/PLNmixture/stability_selection.
>
> test_check("PLNmodels")
*** caught segfault ***
address (nil), cause 'memory not mapped'
Traceback:
1: cpp_test_nlopt()
2: eval_bare(expr, quo_get_env(quo))
3: quasi_label(enquo(object), label, arg = "object")
4: expect_true(cpp_test_nlopt())
5: eval(code, test_env)
6: eval(code, test_env)
7: 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)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: 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) { })
15: test_code(desc, code, env = parent.frame(), reporter = reporter)
16: test_that("PLN: cpp internals are sane", { expect_true(cpp_test_nlopt()) expect_true(cpp_test_packing())})
17: eval(code, test_env)
18: eval(code, test_env)
19: 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)
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
23: doTryCatch(return(expr), name, parentenv, handler)
24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
25: tryCatchList(expr, classes, parentenv, handlers)
26: 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) { })
27: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
28: source_file(path, env = env(env), desc = desc, error_call = error_call)
29: FUN(X[[i]], ...)
30: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(expr, names, parentenv, handlers[[1L]])
33: tryCatchList(expr, classes, parentenv, handlers)
34: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
35: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
36: test_files_serial(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, desc = desc, load_package = load_package, error_call = error_call)
37: 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, load_package = load_package, parallel = parallel)
38: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
39: test_check("PLNmodels")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Import_data.Rmd’ using rmarkdown
--- finished re-building ‘Import_data.Rmd’
--- re-building ‘PLN.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLN_files/figure-html/geometricalInsight-1.png
672x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 73644 bytes
Input file size = 73818 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 55474
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 55474
Output IDAT size = 55474 bytes (18170 bytes decrease)
Output file size = 55552 bytes (18266 bytes = 24.74% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLN_files/figure-html/fitted-1.png
672x480 pixels, 8 bits/pixel, 253 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7493 bytes
Input file size = 8342 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5921
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5921
Output IDAT size = 5921 bytes (1572 bytes decrease)
Output file size = 5999 bytes (2343 bytes = 28.09% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLN_files/figure-html/plot covariance-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 95567 bytes
Input file size = 95777 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 79023
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 79023
Output IDAT size = 79023 bytes (16544 bytes decrease)
Output file size = 79101 bytes (16676 bytes = 17.41% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLN_files/figure-html/weighted-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 10818 bytes
Input file size = 11688 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9157
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9157
Output IDAT size = 9157 bytes (1661 bytes decrease)
Output file size = 9235 bytes (2453 bytes = 20.99% decrease)
--- finished re-building ‘PLN.Rmd’
--- re-building ‘PLNLDA.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNLDA_files/figure-html/vcov-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 69845 bytes
Input file size = 70019 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56181
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56181
Output IDAT size = 56181 bytes (13664 bytes decrease)
Output file size = 56259 bytes (13760 bytes = 19.65% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNLDA_files/figure-html/plot_model-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 100473 bytes
Input file size = 100695 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 77122
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 77122
Output IDAT size = 77122 bytes (23351 bytes decrease)
Output file size = 77200 bytes (23495 bytes = 23.33% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNLDA_files/figure-html/predicted_scores-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 40834 bytes
Input file size = 40960 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33856
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33856
Output IDAT size = 33856 bytes (6978 bytes decrease)
Output file size = 33934 bytes (7026 bytes = 17.15% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNLDA_files/figure-html/plot_model_cov-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 99957 bytes
Input file size = 100179 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 77728
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 77728
Output IDAT size = 77728 bytes (22229 bytes decrease)
Output file size = 77806 bytes (22373 bytes = 22.33% decrease)
--- finished re-building ‘PLNLDA.Rmd’
--- re-building ‘PLNPCA.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNPCA_files/figure-html/plot nocov-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 25197 bytes
Input file size = 25311 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20461
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20461
Output IDAT size = 20461 bytes (4736 bytes decrease)
Output file size = 20539 bytes (4772 bytes = 18.85% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNPCA_files/figure-html/plot nocov-reverse-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 24189 bytes
Input file size = 24291 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20090
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20090
Output IDAT size = 20090 bytes (4099 bytes decrease)
Output file size = 20168 bytes (4123 bytes = 16.97% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNPCA_files/figure-html/map-1.png
768x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 44887 bytes
Input file size = 45025 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39844
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39844
Output IDAT size = 39844 bytes (5043 bytes decrease)
Output file size = 39922 bytes (5103 bytes = 11.33% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNPCA_files/figure-html/sigma-1.png
672x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 76868 bytes
Input file size = 77054 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63973
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63973
Output IDAT size = 63973 bytes (12895 bytes decrease)
Output file size = 64051 bytes (13003 bytes = 16.88% decrease)
Quitting from lines 224-225 [fviz_biplot] (PLNPCA.Rmd)
Error: processing vignette 'PLNPCA.Rmd' failed with diagnostics:
The value of the argument axes is incorrect. The number of axes in the data is: 1. Please try again with axes between 1 - 1
--- failed re-building ‘PLNPCA.Rmd’
--- re-building ‘PLNmixture.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/objective-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8242 bytes
Input file size = 9112 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7391
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7391
Output IDAT size = 7391 bytes (851 bytes decrease)
Output file size = 7469 bytes (1643 bytes = 18.03% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/plot nocov-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 34363 bytes
Input file size = 34489 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26881
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26881
Output IDAT size = 26881 bytes (7482 bytes decrease)
Output file size = 26959 bytes (7530 bytes = 21.83% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/plot nocov-reverse-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 36273 bytes
Input file size = 36399 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27668
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27668
Output IDAT size = 27668 bytes (8605 bytes decrease)
Output file size = 27746 bytes (8653 bytes = 23.77% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/plot clustering-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 17251 bytes
Input file size = 17353 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12977
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12977
Output IDAT size = 12977 bytes (4274 bytes decrease)
Output file size = 13055 bytes (4298 bytes = 24.77% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/plot reordered data-1.png
288x288 pixels, 8 bits/pixel, 252 colors in palette
Input IDAT size = 2497 bytes
Input file size = 3343 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2131
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2131
Output IDAT size = 2131 bytes (366 bytes decrease)
Output file size = 2977 bytes (366 bytes = 10.95% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/predicted_position-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 20662 bytes
Input file size = 20764 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17283
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17283
Output IDAT size = 17283 bytes (3379 bytes decrease)
Output file size = 17361 bytes (3403 bytes = 16.39% decrease)
--- finished re-building ‘PLNmixture.Rmd’
--- re-building ‘PLNnetwork.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNnetwork_files/figure-html/diagnostic-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 23412 bytes
Input file size = 24294 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21544
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21544
Output IDAT size = 21544 bytes (1868 bytes decrease)
Output file size = 21622 bytes (2672 bytes = 11.00% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNnetwork_files/figure-html/plot-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 47309 bytes
Input file size = 47447 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35910
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35910
Output IDAT size = 35910 bytes (11399 bytes decrease)
Output file size = 35988 bytes (11459 bytes = 24.15% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNnetwork_files/figure-html/plot-reverse-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 44173 bytes
Input file size = 44311 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36049
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36049
Output IDAT size = 36049 bytes (8124 bytes decrease)
Output file size = 36127 bytes (8184 bytes = 18.47% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNnetwork_files/figure-html/path_coeff-1.png
672x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 204010 bytes
Input file size = 204376 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 193985
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 193985
Output IDAT size = 193985 bytes (10025 bytes decrease)
Output file size = 194063 bytes (10313 bytes = 5.05% decrease)
Quitting from lines 175-176 [extract models stars] (PLNnetwork.Rmd)
Error: processing vignette 'PLNnetwork.Rmd' failed with diagnostics:
attempt to apply non-function
--- failed re-building ‘PLNnetwork.Rmd’
--- re-building ‘Trichoptera.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/Trichoptera_files/figure-html/count diplay-1.png
672x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 57047 bytes
Input file size = 57197 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44290
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44290
Output IDAT size = 44290 bytes (12757 bytes decrease)
Output file size = 44368 bytes (12829 bytes = 22.43% decrease)
--- finished re-building ‘Trichoptera.Rmd’
SUMMARY: processing the following files failed:
‘PLNPCA.Rmd’ ‘PLNnetwork.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [9s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(PLNmodels)
This is packages 'PLNmodels' version 1.2.0
Use future::plan(multicore/multisession) to speed up PLNPCA/PLNmixture/stability_selection.
>
> test_check("PLNmodels")
*** caught segfault ***
address (nil), cause 'memory not mapped'
Traceback:
1: cpp_test_nlopt()
2: eval_bare(expr, quo_get_env(quo))
3: quasi_label(enquo(object), label, arg = "object")
4: expect_true(cpp_test_nlopt())
5: eval(code, test_env)
6: eval(code, test_env)
7: 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)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: 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) { })
15: test_code(desc, code, env = parent.frame(), reporter = reporter)
16: test_that("PLN: cpp internals are sane", { expect_true(cpp_test_nlopt()) expect_true(cpp_test_packing())})
17: eval(code, test_env)
18: eval(code, test_env)
19: 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)
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
23: doTryCatch(return(expr), name, parentenv, handler)
24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
25: tryCatchList(expr, classes, parentenv, handlers)
26: 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) { })
27: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
28: source_file(path, env = env(env), desc = desc, error_call = error_call)
29: FUN(X[[i]], ...)
30: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(expr, names, parentenv, handlers[[1L]])
33: tryCatchList(expr, classes, parentenv, handlers)
34: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
35: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
36: test_files_serial(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, desc = desc, load_package = load_package, error_call = error_call)
37: 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, load_package = load_package, parallel = parallel)
38: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
39: test_check("PLNmodels")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Import_data.Rmd’ using rmarkdown
--- finished re-building ‘Import_data.Rmd’
--- re-building ‘PLN.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLN_files/figure-html/geometricalInsight-1.png
672x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 73644 bytes
Input file size = 73818 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 55474
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 55474
Output IDAT size = 55474 bytes (18170 bytes decrease)
Output file size = 55552 bytes (18266 bytes = 24.74% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLN_files/figure-html/fitted-1.png
672x480 pixels, 8 bits/pixel, 253 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7493 bytes
Input file size = 8342 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5921
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5921
Output IDAT size = 5921 bytes (1572 bytes decrease)
Output file size = 5999 bytes (2343 bytes = 28.09% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLN_files/figure-html/plot covariance-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 95567 bytes
Input file size = 95777 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 79023
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 79023
Output IDAT size = 79023 bytes (16544 bytes decrease)
Output file size = 79101 bytes (16676 bytes = 17.41% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLN_files/figure-html/weighted-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 10818 bytes
Input file size = 11688 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9157
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9157
Output IDAT size = 9157 bytes (1661 bytes decrease)
Output file size = 9235 bytes (2453 bytes = 20.99% decrease)
--- finished re-building ‘PLN.Rmd’
--- re-building ‘PLNLDA.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNLDA_files/figure-html/vcov-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 69845 bytes
Input file size = 70019 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56181
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56181
Output IDAT size = 56181 bytes (13664 bytes decrease)
Output file size = 56259 bytes (13760 bytes = 19.65% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNLDA_files/figure-html/plot_model-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 100473 bytes
Input file size = 100695 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 77122
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 77122
Output IDAT size = 77122 bytes (23351 bytes decrease)
Output file size = 77200 bytes (23495 bytes = 23.33% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNLDA_files/figure-html/predicted_scores-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 40834 bytes
Input file size = 40960 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33856
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33856
Output IDAT size = 33856 bytes (6978 bytes decrease)
Output file size = 33934 bytes (7026 bytes = 17.15% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNLDA_files/figure-html/plot_model_cov-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 99957 bytes
Input file size = 100179 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 77728
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 77728
Output IDAT size = 77728 bytes (22229 bytes decrease)
Output file size = 77806 bytes (22373 bytes = 22.33% decrease)
--- finished re-building ‘PLNLDA.Rmd’
--- re-building ‘PLNPCA.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNPCA_files/figure-html/plot nocov-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 25197 bytes
Input file size = 25311 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20461
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20461
Output IDAT size = 20461 bytes (4736 bytes decrease)
Output file size = 20539 bytes (4772 bytes = 18.85% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNPCA_files/figure-html/plot nocov-reverse-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 24189 bytes
Input file size = 24291 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20090
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20090
Output IDAT size = 20090 bytes (4099 bytes decrease)
Output file size = 20168 bytes (4123 bytes = 16.97% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNPCA_files/figure-html/map-1.png
768x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 44209 bytes
Input file size = 44347 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39186
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39186
Output IDAT size = 39186 bytes (5023 bytes decrease)
Output file size = 39264 bytes (5083 bytes = 11.46% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNPCA_files/figure-html/sigma-1.png
672x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 76868 bytes
Input file size = 77054 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63973
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63973
Output IDAT size = 63973 bytes (12895 bytes decrease)
Output file size = 64051 bytes (13003 bytes = 16.88% decrease)
Quitting from lines 224-225 [fviz_biplot] (PLNPCA.Rmd)
Error: processing vignette 'PLNPCA.Rmd' failed with diagnostics:
The value of the argument axes is incorrect. The number of axes in the data is: 1. Please try again with axes between 1 - 1
--- failed re-building ‘PLNPCA.Rmd’
--- re-building ‘PLNmixture.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/objective-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8242 bytes
Input file size = 9112 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7391
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7391
Output IDAT size = 7391 bytes (851 bytes decrease)
Output file size = 7469 bytes (1643 bytes = 18.03% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/plot nocov-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 34363 bytes
Input file size = 34489 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26881
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26881
Output IDAT size = 26881 bytes (7482 bytes decrease)
Output file size = 26959 bytes (7530 bytes = 21.83% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/plot nocov-reverse-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 36273 bytes
Input file size = 36399 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27668
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27668
Output IDAT size = 27668 bytes (8605 bytes decrease)
Output file size = 27746 bytes (8653 bytes = 23.77% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/plot clustering-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 16894 bytes
Input file size = 16996 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12807
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12807
Output IDAT size = 12807 bytes (4087 bytes decrease)
Output file size = 12885 bytes (4111 bytes = 24.19% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/plot reordered data-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Input IDAT size = 2522 bytes
Input file size = 3380 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2150
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2150
Output IDAT size = 2150 bytes (372 bytes decrease)
Output file size = 3008 bytes (372 bytes = 11.01% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/predicted_position-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 20289 bytes
Input file size = 20391 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17010
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17010
Output IDAT size = 17010 bytes (3279 bytes decrease)
Output file size = 17088 bytes (3303 bytes = 16.20% decrease)
--- finished re-building ‘PLNmixture.Rmd’
--- re-building ‘PLNnetwork.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNnetwork_files/figure-html/diagnostic-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 23412 bytes
Input file size = 24294 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21544
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21544
Output IDAT size = 21544 bytes (1868 bytes decrease)
Output file size = 21622 bytes (2672 bytes = 11.00% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNnetwork_files/figure-html/plot-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 47309 bytes
Input file size = 47447 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35910
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35910
Output IDAT size = 35910 bytes (11399 bytes decrease)
Output file size = 35988 bytes (11459 bytes = 24.15% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNnetwork_files/figure-html/plot-reverse-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 44173 bytes
Input file size = 44311 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36049
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36049
Output IDAT size = 36049 bytes (8124 bytes decrease)
Output file size = 36127 bytes (8184 bytes = 18.47% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNnetwork_files/figure-html/path_coeff-1.png
672x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 204010 bytes
Input file size = 204376 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 193985
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 193985
Output IDAT size = 193985 bytes (10025 bytes decrease)
Output file size = 194063 bytes (10313 bytes = 5.05% decrease)
Quitting from lines 175-176 [extract models stars] (PLNnetwork.Rmd)
Error: processing vignette 'PLNnetwork.Rmd' failed with diagnostics:
attempt to apply non-function
--- failed re-building ‘PLNnetwork.Rmd’
--- re-building ‘Trichoptera.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/Trichoptera_files/figure-html/count diplay-1.png
672x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 57047 bytes
Input file size = 57197 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44290
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44290
Output IDAT size = 44290 bytes (12757 bytes decrease)
Output file size = 44368 bytes (12829 bytes = 22.43% decrease)
--- finished re-building ‘Trichoptera.Rmd’
SUMMARY: processing the following files failed:
‘PLNPCA.Rmd’ ‘PLNnetwork.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Import_data.Rmd’ using rmarkdown
--- finished re-building ‘Import_data.Rmd’
--- re-building ‘PLN.Rmd’ using rmarkdown
--- finished re-building ‘PLN.Rmd’
--- re-building ‘PLNLDA.Rmd’ using rmarkdown
--- finished re-building ‘PLNLDA.Rmd’
--- re-building ‘PLNPCA.Rmd’ using rmarkdown
Quitting from lines 35-39 [requirement] (PLNPCA.Rmd)
Error: processing vignette 'PLNPCA.Rmd' failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building ‘PLNPCA.Rmd’
--- re-building ‘PLNmixture.Rmd’ using rmarkdown
Quitting from lines 38-40 [requirement] (PLNmixture.Rmd)
Error: processing vignette 'PLNmixture.Rmd' failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building ‘PLNmixture.Rmd’
--- re-building ‘PLNnetwork.Rmd’ using rmarkdown
--- finished re-building ‘PLNnetwork.Rmd’
--- re-building ‘Trichoptera.Rmd’ using rmarkdown
--- finished re-building ‘Trichoptera.Rmd’
SUMMARY: processing the following files failed:
‘PLNPCA.Rmd’ ‘PLNmixture.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-macos-x86_64
Version: 1.2.0
Check: installed package size
Result: NOTE
installed size is 17.3Mb
sub-directories of 1Mb or more:
data 1.4Mb
doc 2.1Mb
libs 12.1Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.