Last updated on 2024-11-02 23:48:20 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.9.17 | 12.50 | 125.39 | 137.89 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.9.17 | 8.20 | 90.45 | 98.65 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.9.17 | 228.48 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 0.9.17 | 220.26 | NOTE | |||
| r-devel-windows-x86_64 | 0.9.17 | 17.00 | 184.00 | 201.00 | NOTE | |
| r-patched-linux-x86_64 | 0.9.17 | 17.68 | 117.48 | 135.16 | NOTE | |
| r-release-linux-x86_64 | 0.9.17 | 10.56 | 98.26 | 108.82 | ERROR | |
| r-release-macos-arm64 | 0.9.17 | 88.00 | NOTE | |||
| r-release-macos-x86_64 | 0.9.17 | 136.00 | NOTE | |||
| r-release-windows-x86_64 | 0.9.17 | 16.00 | 176.00 | 192.00 | NOTE | |
| r-oldrel-macos-arm64 | 0.9.17 | 92.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.9.17 | 158.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 0.9.17 | 19.00 | 218.00 | 237.00 | OK |
Version: 0.9.17
Check: Rd files
Result: NOTE
checkRd: (-1) JobCollection.Rd:41: Lost braces
41 | \item{namespaces}{code{character} with required packages to load via \code{\link[base]{requireNamespace}}.}
| ^
checkRd: (-1) addAlgorithm.Rd:31: Lost braces
31 | Algorithms are functions which get the code{data} part as well as the problem instance (the return value of the
| ^
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
Version: 0.9.17
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
JoinTables.Rd: data.table
Worker.Rd: R6Class
addExperiments.Rd: data.table
batchMap.Rd: data.table
batchMapResults.Rd: data.table
batchReduce.Rd: data.table
estimateRuntimes.Rd: data.table
findJobs.Rd: data.table
getErrorMessages.Rd: data.table
getJobTable.Rd: data.table
grepLogs.Rd: data.table
killJobs.Rd: data.table
removeExperiments.Rd: data.table
resetJobs.Rd: data.table
runHook.Rd: data.table
submitJobs.Rd: data.table
summarizeExperiments.Rd: data.table
unwrap.Rd: data.table
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: 0.9.17
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘ranger’
Flavor: r-release-linux-x86_64
Version: 0.9.17
Check: examples
Result: ERROR
Running examples in ‘batchtools-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estimateRuntimes
> ### Title: Estimate Remaining Runtimes
> ### Aliases: estimateRuntimes print.RuntimeEstimate
>
> ### ** Examples
>
> ## Don't show:
> batchtools:::example_push_temp(1)
> ## End(Don't show)
> # Create a simple toy registry
> set.seed(1)
> tmp = makeExperimentRegistry(file.dir = NA, make.default = FALSE, seed = 1)
No readable configuration file found
Created registry in '/home/hornik/tmp/scratch/RtmpkIqTie/registry3950f321200b6c' using cluster functions 'Interactive'
> addProblem(name = "iris", data = iris, fun = function(data, ...) nrow(data), reg = tmp)
Adding problem 'iris'
> addAlgorithm(name = "nrow", function(instance, ...) nrow(instance), reg = tmp)
Adding algorithm 'nrow'
> addAlgorithm(name = "ncol", function(instance, ...) ncol(instance), reg = tmp)
Adding algorithm 'ncol'
> addExperiments(algo.designs = list(nrow = data.table::CJ(x = 1:50, y = letters[1:5])), reg = tmp)
Adding 250 experiments ('iris'[1] x 'nrow'[250] x repls[1]) ...
> addExperiments(algo.designs = list(ncol = data.table::CJ(x = 1:50, y = letters[1:5])), reg = tmp)
Adding 250 experiments ('iris'[1] x 'ncol'[250] x repls[1]) ...
>
> # We use the job parameters to predict runtimes
> tab = unwrap(getJobPars(reg = tmp))
>
> # First we need to submit some jobs so that the forest can train on some data.
> # Thus, we just sample some jobs from the registry while grouping by factor variables.
> library(data.table)
> ids = tab[, .SD[sample(nrow(.SD), 5)], by = c("problem", "algorithm", "y")]
> setkeyv(ids, "job.id")
> submitJobs(ids, reg = tmp)
Submitting 50 jobs in 50 chunks using cluster functions 'Interactive' ...
> waitForJobs(reg = tmp)
[1] TRUE
>
> # We "simulate" some more realistic runtimes here to demonstrate the functionality:
> # - Algorithm "ncol" is 5 times more expensive than "nrow"
> # - x has no effect on the runtime
> # - If y is "a" or "b", the runtimes are really high
> runtime = function(algorithm, x, y) {
+ ifelse(algorithm == "nrow", 100L, 500L) + 1000L * (y %in% letters[1:2])
+ }
> tmp$status[ids, done := done + tab[ids, runtime(algorithm, x, y)]]
> rjoin(sjoin(tab, ids), getJobStatus(ids, reg = tmp)[, c("job.id", "time.running")])
Key: <job.id>
job.id problem algorithm x y time.running
<int> <char> <char> <int> <char> <difftime>
1: 32 iris nrow 7 b 1100.0021 secs
2: 42 iris nrow 9 b 1100.0061 secs
3: 47 iris nrow 10 b 1100.0061 secs
4: 66 iris nrow 14 a 1100.0020 secs
5: 73 iris nrow 15 c 100.0020 secs
6: 75 iris nrow 15 e 100.0018 secs
7: 86 iris nrow 18 a 1100.0017 secs
8: 100 iris nrow 20 e 100.0018 secs
9: 101 iris nrow 21 a 1100.0062 secs
10: 103 iris nrow 21 c 100.0019 secs
11: 123 iris nrow 25 c 100.0018 secs
12: 125 iris nrow 25 e 100.0017 secs
13: 161 iris nrow 33 a 1100.0017 secs
14: 165 iris nrow 33 e 100.0020 secs
15: 169 iris nrow 34 d 100.0017 secs
16: 183 iris nrow 37 c 100.0019 secs
17: 184 iris nrow 37 d 100.0062 secs
18: 203 iris nrow 41 c 100.0017 secs
19: 207 iris nrow 42 b 1100.0018 secs
20: 209 iris nrow 42 d 100.0019 secs
21: 220 iris nrow 44 e 100.0061 secs
22: 227 iris nrow 46 b 1100.0018 secs
23: 229 iris nrow 46 d 100.0017 secs
24: 231 iris nrow 47 a 1100.0019 secs
25: 244 iris nrow 49 d 100.0060 secs
26: 260 iris ncol 2 e 500.0017 secs
27: 276 iris ncol 6 a 1500.0018 secs
28: 278 iris ncol 6 c 500.0018 secs
29: 279 iris ncol 6 d 500.0019 secs
30: 296 iris ncol 10 a 1500.0018 secs
31: 320 iris ncol 14 e 500.0017 secs
32: 340 iris ncol 18 e 500.0017 secs
33: 347 iris ncol 20 b 1500.0016 secs
34: 363 iris ncol 23 c 500.0018 secs
35: 369 iris ncol 24 d 500.0016 secs
36: 373 iris ncol 25 c 500.0017 secs
37: 387 iris ncol 28 b 1500.0017 secs
38: 410 iris ncol 32 e 500.0020 secs
39: 421 iris ncol 35 a 1500.0016 secs
40: 436 iris ncol 38 a 1500.0018 secs
41: 444 iris ncol 39 d 500.0018 secs
42: 448 iris ncol 40 c 500.0064 secs
43: 456 iris ncol 42 a 1500.0063 secs
44: 459 iris ncol 42 d 500.0019 secs
45: 467 iris ncol 44 b 1500.0060 secs
46: 468 iris ncol 44 c 500.0063 secs
47: 475 iris ncol 45 e 500.0061 secs
48: 482 iris ncol 47 b 1500.0060 secs
49: 492 iris ncol 49 b 1500.0020 secs
50: 499 iris ncol 50 d 500.0061 secs
job.id problem algorithm x y time.running
>
> # Estimate runtimes:
> est = estimateRuntimes(tab, reg = tmp)
Error in estimateRuntimes(tab, reg = tmp) :
Please install package 'ranger' for runtime estimation
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.9.17
Check: tests
Result: ERROR
Running ‘testthat.R’ [31s/59s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
>
> library(testthat)
> library(batchtools)
>
> test_check("batchtools")
### [bt]: Setting seed to 29402 ...
### [bt]: Setting seed to 3080 ...
### [bt]: Setting seed to 3082 ...
### [bt]: Setting seed to 3081 ...
[ FAIL 1 | WARN 0 | SKIP 7 | PASS 1452 ]
══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test_ClusterFunctionsSSH.R:4:3', 'test_memory.R:4:3',
'test_sweepRegistry.R:37:3'
• Test requires killJobs (2): 'test_killJobs.R:3:3', 'test_waitForJobs.R:14:3'
• Test requires listJobsRunning (1): 'test_findJobs.R:79:3'
• manual test (1): 'test_manual.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_estimateRuntimes.R:20:3'): estimateRuntimes ────────────────────
Error in `estimateRuntimes(tab, reg = reg)`: Please install package 'ranger' for runtime estimation
Backtrace:
▆
1. └─batchtools::estimateRuntimes(tab, reg = reg) at test_estimateRuntimes.R:20:3
[ FAIL 1 | WARN 0 | SKIP 7 | PASS 1452 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.9.17
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘batchtools.Rmd’ using rmarkdown
Quitting from lines 383-389 [unnamed-chunk-23] (batchtools.Rmd)
Error: processing vignette 'batchtools.Rmd' failed with diagnostics:
there is no package called 'ranger'
--- failed re-building ‘batchtools.Rmd’
SUMMARY: processing the following file failed:
‘batchtools.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.9.17
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘doMPI’
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 0.9.17
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘Rmpi’
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64