Last updated on 2023-12-07 12:49:43 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.0.2 | 22.21 | 309.24 | 331.45 | OK | |
| r-devel-linux-x86_64-debian-gcc | 3.0.2 | 15.39 | 171.38 | 186.77 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 3.0.2 | 396.66 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 3.0.2 | 395.62 | OK | |||
| r-devel-windows-x86_64 | 3.0.2 | 18.00 | 271.00 | 289.00 | OK | |
| r-patched-linux-x86_64 | 3.0.2 | 17.47 | 299.93 | 317.40 | OK | |
| r-release-linux-x86_64 | 3.0.2 | 14.38 | 291.10 | 305.48 | OK | |
| r-release-macos-arm64 | 3.0.2 | 107.00 | OK | |||
| r-release-macos-x86_64 | 3.0.2 | 221.00 | OK | |||
| r-release-windows-x86_64 | 3.0.2 | 25.00 | 313.00 | 338.00 | OK | |
| r-oldrel-macos-arm64 | 3.0.2 | 113.00 | OK | |||
| r-oldrel-macos-x86_64 | 3.0.2 | 159.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 3.0.2 | 24.00 | 303.00 | 327.00 | OK |
Version: 3.0.2
Check: examples
Result: ERROR
Running examples in ‘RGCCA-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: print.rgcca
> ### Title: Print a fitted object from the RGCCA package
> ### Aliases: print.rgcca print.rgcca_cv print.rgcca_permutation
> ### print.rgcca_bootstrap print.rgcca_stability
>
> ### ** Examples
>
> ## Printing of an rgcca object
> data(Russett)
> blocks <- list(
+ agriculture = Russett[, seq(3)],
+ industry = Russett[, 4:5],
+ politic = Russett[, 6:8]
+ )
> C <- matrix(c(0, 0, 1, 0, 0, 1, 1, 1, 0), 3, 3)
> res <- rgcca(blocks,
+ connection = C, ncomp = rep(2, 3), tau = c(1, 1, 1),
+ scheme = "factorial", scale = TRUE, verbose = FALSE
+ )
> print(res)
Fitted RGCCA model.
The algorithm converged to a stationnary point:
- After 2 iterations for component 1.
- After 6 iterations for component 2.
>
> ## Printing of an rgcca_cv object
> res <- rgcca_cv(blocks,
+ response = 3, method = "rgcca", par_type = "tau",
+ par_value = c(0, 0.2, 0.3), n_run = 1, n_cores = 1,
+ verbose = TRUE
+ )
> print(res)
RGCCA cross-validation object obtained with 10 sets of parameters using 5 folds.
Regression was performed using lm model.
>
> ## Printing of an rgcca_permutation object
> perm.out <- rgcca_permutation(blocks,
+ par_type = "tau",
+ n_perms = 5, n_cores = 1,
+ verbose = TRUE
+ )
Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 3.0.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [22s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(RGCCA)
>
> test_check("RGCCA")
[ FAIL 10 | WARN 0 | SKIP 41 | PASS 824 ]
══ Skipped tests (41) ══════════════════════════════════════════════════════════
• On CRAN (6): 'test_print_call.R:11:3', 'test_print_call.R:24:3',
'test_print_comp.R:10:3', 'test_print_comp.R:19:3', 'test_print_comp.R:28:3',
'test_print_comp.R:37:3'
• as.logical(Sys.getenv("TEST_SNAPSHOTS")) is not TRUE (34):
'test_plot.rgcca.r:27:3', 'test_plot.rgcca.r:36:3', 'test_plot.rgcca.r:47:3',
'test_plot.rgcca.r:55:3', 'test_plot.rgcca.r:65:3', 'test_plot.rgcca.r:72:3',
'test_plot.rgcca.r:79:3', 'test_plot.rgcca.r:86:3', 'test_plot.rgcca.r:93:3',
'test_plot.rgcca.r:100:3', 'test_plot.rgcca.r:109:3',
'test_plot.rgcca_bootstrap.R:30:3', 'test_plot.rgcca_bootstrap.R:37:3',
'test_plot.rgcca_stability.R:16:3', 'test_print.rgcca.R:10:3',
'test_print.rgcca.R:19:3', 'test_print.rgcca_bootstrap.R:13:3',
'test_print.rgcca_cv.R:17:3', 'test_print.rgcca_cv.R:30:3',
'test_print.rgcca_stability.R:13:3', 'test_summary.rgcca.r:11:3',
'test_summary.rgcca.r:20:3', 'test_summary.rgcca.r:30:3',
'test_summary.rgcca.r:39:3', 'test_summary.rgcca.r:49:3',
'test_summary.rgcca_bootstrap.r:12:3', 'test_summary.rgcca_bootstrap.r:21:3',
'test_summary.rgcca_cv.R:17:3', 'test_summary.rgcca_cv.R:30:3',
'test_summary.rgcca_cv.R:43:3', 'test_summary.rgcca_cv.R:56:3',
'test_summary.rgcca_permutation.R:12:3',
'test_summary.rgcca_permutation.R:24:3',
'test_summary.rgcca_stability.R:13:3'
• gliomaData cannot be loaded (1): 'test_rgcca_predict.r:54:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_plot.rgcca_cv.R:15:1'): (code run outside of `test_that()`) ────
<1/simpleError/error/condition>
Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test_plot.rgcca_cv.R:15:1
2. │ └─base::withCallingHandlers(...)
3. └─RGCCA::rgcca_cv(...)
4. └─RGCCA:::set_parameter_grid(...)
5. └─RGCCA (local) check_param_type(par_value, blocks)
6. └─RGCCA:::stop_rgcca(...)
── Error ('test_plot.rgcca_permutation.r:10:1'): (code run outside of `test_that()`) ──
<1/simpleError/error/condition>
Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
Backtrace:
▆
1. └─RGCCA::rgcca_permutation(...) at test_plot.rgcca_permutation.r:10:1
2. └─RGCCA:::set_parameter_grid(...)
3. └─RGCCA (local) check_param_type(par_value, blocks)
4. └─RGCCA:::stop_rgcca(...)
── Error ('test_print.rgcca_permutation.R:11:1'): (code run outside of `test_that()`) ──
<1/simpleError/error/condition>
Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
Backtrace:
▆
1. └─RGCCA::rgcca_permutation(...) at test_print.rgcca_permutation.R:11:1
2. └─RGCCA:::set_parameter_grid(...)
3. └─RGCCA (local) check_param_type(par_value, blocks)
4. └─RGCCA:::stop_rgcca(...)
── Error ('test_rgcca_cv.r:52:3'): rgcca_cv generates a warning if tau is null and block has more
columns than rows ──
<1/simpleError/error/condition>
Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 4).
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_rgcca_cv.r:52:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─RGCCA::rgcca_cv(bad_blocks, response = 4, prediction_model = "lm")
7. └─RGCCA:::set_parameter_grid(...)
8. └─RGCCA (local) check_param_type(par_value, blocks)
9. └─RGCCA:::stop_rgcca(...)
── Error ('test_rgcca_cv.r:61:3'): rgcca_cv changes par_type to sparsity if a sparse method is given
with par_type = 'tau' ──
<1/simpleError/error/condition>
Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
Backtrace:
▆
1. └─RGCCA::rgcca_cv(...) at test_rgcca_cv.r:61:3
2. └─RGCCA:::set_parameter_grid(...)
3. └─RGCCA (local) check_param_type(par_value, blocks)
4. └─RGCCA:::stop_rgcca(...)
── Error ('test_rgcca_cv.r:74:3'): rgcca_cv computes k * n_run scores per parameter value ──
<1/simpleError/error/condition>
Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
Backtrace:
▆
1. └─RGCCA::rgcca_cv(...) at test_rgcca_cv.r:74:3
2. └─RGCCA:::set_parameter_grid(...)
3. └─RGCCA (local) check_param_type(par_value, blocks)
4. └─RGCCA:::stop_rgcca(...)
── Error ('test_rgcca_permutation.R:18:3'): rgcca_permutation changes par_type to sparsity if a sparse method is
given with par_type = 'tau' ──
<1/simpleError/error/condition>
Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
Backtrace:
▆
1. └─RGCCA::rgcca_permutation(...) at test_rgcca_permutation.R:18:3
2. └─RGCCA:::set_parameter_grid(...)
3. └─RGCCA (local) check_param_type(par_value, blocks)
4. └─RGCCA:::stop_rgcca(...)
── Error ('test_rgcca_permutation.R:32:3'): rgcca_permutation computes n_perms permuted scores and one non
permuted score per parameter value ──
<1/simpleError/error/condition>
Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
Backtrace:
▆
1. └─RGCCA::rgcca_permutation(...) at test_rgcca_permutation.R:32:3
2. └─RGCCA:::set_parameter_grid(...)
3. └─RGCCA (local) check_param_type(par_value, blocks)
4. └─RGCCA:::stop_rgcca(...)
── Error ('test_rgcca_permutation.R:59:3'): rgcca imports the parameters from a permutation object ──
<1/simpleError/error/condition>
Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
Backtrace:
▆
1. └─RGCCA::rgcca_permutation(...) at test_rgcca_permutation.R:59:3
2. └─RGCCA:::set_parameter_grid(...)
3. └─RGCCA (local) check_param_type(par_value, blocks)
4. └─RGCCA:::stop_rgcca(...)
── Error ('test_set_parameter_grid.R:44:3'): set_parameter_grid returns a valid grid of parameters when par_value
is NULL ──
<1/simpleError/error/condition>
Error: wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
Backtrace:
▆
1. └─RGCCA:::set_parameter_grid(...) at test_set_parameter_grid.R:44:3
2. └─RGCCA (local) check_param_type(par_value, blocks)
3. └─RGCCA:::stop_rgcca(...)
[ FAIL 10 | WARN 0 | SKIP 41 | PASS 824 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 3.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘RGCCA.Rmd’ using rmarkdown
Quitting from lines 786-792 [unnamed-chunk-12] (RGCCA.Rmd)
Error: processing vignette 'RGCCA.Rmd' failed with diagnostics:
wrong shape. If par_value is a matrix or a dataframe,it must have as many columns as there are blocks (i.e. 3).
--- failed re-building ‘RGCCA.Rmd’
SUMMARY: processing the following file failed:
‘RGCCA.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 3.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘RGCCA.Rmd’ using rmarkdown
! pdfTeX error (ext4): \pdfendlink ended up in different nesting level than \pd
fstartlink.
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.518
Error: processing vignette 'RGCCA.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/high-sierra-x86_64/results/4.2/RGCCA.Rcheck/vign_test/RGCCA/vignettes/RGCCA.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See RGCCA.log for more info.
--- failed re-building ‘RGCCA.Rmd’
SUMMARY: processing the following file failed:
‘RGCCA.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-x86_64